@droftarts
This is the configuration before drives.

G90                                                ; send absolute coordinates...
M83                                                ; ...but relative extruder moves
M550 P"Drukarka3D"                                 ; set printer name

; Wait a moment for the CAN expansion boards to start
G4 S2

; Network
M552 P192.168.1.15 S1                           ; enable network and set IP address
M553 P255.255.255.0                             ; set netmask
M554 P192.168.1.1                               ; set gateway
M586 P0 S1                                      ; enable HTTP
M586 P1 S0                                      ; disable FTP
M586 P2 S0                                      ; disable Telnet

And regarding the "odd homing", of course you are right, I was only trying to move the the U axis when T1 was chosen. When moving X, it works well. Thank you.

@droftarts
Changes applied, but still have to tinker with the M671.

After choosing the Tool1, but not printing, the only thing that is odd is, when I move the T1 for example to the middle of the bed and move any other axis, the carriage U goes to it's homing position. When this happens and I move U axis even for a 1mm, the carriege goes back to the position before this "odd homing"

When I try to print with T1 only, it goes to the end of the axis and hit the second carriage and prints the line there.

I also was chaging the offset for the U axis a bit to be more precise.

; Drives
M584 X0.2 Y40.0 Z0.0:0.1 E0.5:0.4 U0.3                     ; set drive mapping
M569 P0.2 S1                                       ; physical drive 0.2 goes forwards
M569 P40.0 S1 R0 T5:5:5:5							; physical drive 40.0 goes forwards
M569 P0.1 S0
M569 P0.3 S1
M569 P0.0 S0                                       ; physical drive 0.0 goes forwards
M569 P0.5 S1                                       ; physical drive 0.5 goes forwards
M569 P0.4 S1                                       ; physical drive 0.4 goes forwards
M671 X-20:220 Y0:0 S0.5
M350 X16 Y16 Z16 E16:16 U16 I0                         ; configure microstepping with interpolation
M92 X100.35 Y80.10 Z320.00 E896.15:896.15 U100.35         ; set steps per mm
M566 X500.00 Y500.00 Z1000.00 E500.00:500.00 U500.00         ; set maximum instantaneous speed changes (mm/min)
M203 X12000.00 Y12000.00 Z800.00 E12000.01:12000.01 U12000.00    ; set maximum speeds (mm/min)
M201 X500.00 Y500.00 Z200.00 E500.01:500.01 U500.00        ; set accelerations (mm/s^2)
M906 X1200 Y3000 Z900 E1900:1900 U1200 I30                ; set motor currents (mA) and motor idle factor in per cent
M84 S300000                                            ; Set idle timeout

M572 D0:1 S0.2                  ; set extruder 0, 1 and 2 pressure advance to 0.2 seconds (RepRapFirmware 1.20 and later)

; Axis Limits
M208 X-5:450 Y0:500 Z0:475 U40:585                                   ; set axis minima/maxima

; Endstops
M574 X1 S1 P"io0.in"                               ; configure switch-type (e.g. microswitch) endstop for low end on X via pin io0.in
M574 Y1 S1 P"io2.in"                               ; configure switch-type (e.g. microswitch) endstop for low end on Y via pin io2.in
M574 Z2 S1 P"io5.in+io4.in"                               ; configure switch-type (e.g. microswitch) endstop for high end on Z via pin io4.in
M574 U2 S1 P"io3.in"

; Z-Probe
M558 P0 H5 F120 T6000                              ; disable Z probe but set dive height, probe speed and travel speed
M557 X15:215 Y15:195 S20                           ; define mesh grid

; Heaters
M308 S0 P"temp2" Y"thermistor" T100000 B4138       ; configure sensor 0 as thermistor on pin temp2
M950 H0 C"out0" T0                                 ; create bed heater output on out0 and map it to sensor 0
M307 H0 R5.187 K0.400:0.000 D41.47 E1.35 S0.00 B1  ; enable bang-bang mode for the bed heater and set PWM limit
M140 H0                                            ; map heated bed to heater 0
M143 H0 S100                                       ; set temperature limit for heater 0 to 100C
M308 S2 P"temp0" Y"thermistor" T100000 B4138       ; configure sensor 1 as thermistor on pin temp0
M950 H2 C"out2" T2                                 ; create nozzle heater output on out1 and map it to sensor 1
M307 H2 R2.962 K0.727:0.000 D8.70 E1.35 S1.00 B0
M307 H2 S240                                       ; set temperature limit for heater 1 to 240C
M308 S1 P"temp1" Y"thermistor" T100000 B4138       ; configure sensor 1 as thermistor on pin temp1
M950 H1 C"out1" T1                                 ; create nozzle heater output on out1 and map it to sensor 1
M307 H1 R80.490 K900:0.0 D20.02 E1.35 S0.05 B0 I0.5 V23.8                                   ; disable bang-bang mode for heater  and set PWM limit
M143 H1 S260                                       ; set temperature limit for heater 1 to 240C

; Fans
M950 F0 C"out9" Q500                               ; create fan 0 on pin out7 and set its frequency
M106 P0 S1 H1 T45                                  ; set fan 0 value. Thermostatic control is turned on
M950 F1 C"out8" Q500                               ; create fan 1 on pin out8 and set its frequency
M106 P1 S1 H1 T45                                  ; set fan 1 value. Thermostatic control is turned on
M950 F2 C"out7" Q500                               ; create fan 1 on pin out8 and set its frequency
M106 P2 S1 H1 T45                                  ; set fan 1 value. Thermostatic control is turned on
M950 F3 C"out4" Q500                               ; create fan 1 on pin out8 and set its frequency
M106 P3 S1 H0 T28:40                                  ; set fan 1 value. Thermostatic control is turned on
M950 F4 C"out5" Q500                               ; create fan 1 on pin out8 and set its frequency
M106 P4 S1 H1 T120                                  ; set fan 1 value. Thermostatic control is turned on

; Tools
M563 P0 D0 H1 F0                                 ; define tool 0
G10 P0 X0 Y0 Z0                                    ; set tool 0 axis offsets
G10 P0 R215 S215                                       ; set initial tool 0 active and standby temperatures to 70C

M563 P1 D1 H2 X3 F1                                    ; define tool 1
G10 P1 X0 Y-1 Z0                                    ; set tool 1 axis offsets
G10 P1 R215 S215                                       ; set initial tool 1 active and standby temperatures to 70C

; Create a tool that prints 2 copies of the object using both carriages
M563 P2 D0:1 H1:2 X0:3 F0:1 ; tool 2 uses both extruders, hot end heaters and fans, and maps X to both X and U
G10 P2 X112.5 Y0 U-112.5 S215 R215 ; set tool offsets and temperatures
M567 P2 E1:1 ; set mix ratio 100% on both extruders

; tfree0.g

M83              ; relative extruder movement
M106 S0          ; turn off our print cooling fan
G91              ; relative axis movement
G1 Z5 F500       ; up 3mm
G90              ; absolute axis movement
G1 H2 X-5 F6000 ; park the X carriage at -5mm

; tfree1.g

M83              ; relative extruder movement
M106 S0          ; turn off our print cooling fan
G91              ; relative axis movement
G1 Z5 F500       ; up 3mm
G90              ; absolute axis movement
G1 H2 U535 F6000 ; park the U carriage at 535mm
M579 

@droftarts

; Drives
M584 X0.2 Y40.0 Z0.0:0.1 E0.5:0.4 U0.3                     ; set drive mapping
M569 P0.2 S1                                       ; physical drive 0.2 goes forwards
M569 P40.0 S1 R0 T5:5:5:5							; physical drive 40.0 goes forwards
M569 P0.1 S0
M569 P0.3 S1
M569 P0.0 S0                                       ; physical drive 0.0 goes forwards
M569 P0.5 S1                                       ; physical drive 0.5 goes forwards
M569 P0.4 S1                                       ; physical drive 0.4 goes forwards
M671 X-20:220 Y0:0 S0.5
M208 X-5:205 Y0:200 U-5:205
M350 X16 Y16 Z16 E16:16 U16 I0                         ; configure microstepping with interpolation
M92 X100.35 Y80.10 Z320.00:320.00 E896.15:896.15 U100.35         ; set steps per mm
M566 X500.00 Y500.00 Z1000.00:1000.00 E500.00:500.00 U500.00         ; set maximum instantaneous speed changes (mm/min)
M203 X12000.00 Y12000.00 Z800.00:800.00 E12000.01:12000.01 U12000.00    ; set maximum speeds (mm/min)
M201 X500.00 Y500.00 Z200.00:200.00 E500.01:500.01 U500.00        ; set accelerations (mm/s^2)
M906 X1200 Y3000 Z900:900 E1900:1900 U1200 I30                ; set motor currents (mA) and motor idle factor in per cent
M84 S300000                                            ; Set idle timeout

M572 D0:1 S0.2                  ; set extruder 0, 1 and 2 pressure advance to 0.2 seconds (RepRapFirmware 1.20 and later)

; Axis Limits
M208 X-5:450 Y0:500 Z0:475 U20:538                                   ; set axis minima/maxima

; Endstops
M574 X1 S1 P"io0.in"                               ; configure switch-type (e.g. microswitch) endstop for low end on X via pin io0.in
M574 Y1 S1 P"io2.in"                               ; configure switch-type (e.g. microswitch) endstop for low end on Y via pin io2.in
M574 Z2 S1 P"io5.in+io4.in"                               ; configure switch-type (e.g. microswitch) endstop for high end on Z via pin io4.in
M574 U2 S1 P"io3.in"

; Z-Probe
M558 P0 H5 F120 T6000                              ; disable Z probe but set dive height, probe speed and travel speed
M557 X15:215 Y15:195 S20                           ; define mesh grid

; Heaters
M308 S0 P"temp2" Y"thermistor" T100000 B4138       ; configure sensor 0 as thermistor on pin temp2
M950 H0 C"out0" T0                                 ; create bed heater output on out0 and map it to sensor 0
M307 H0 R5.187 K0.400:0.000 D41.47 E1.35 S0.00 B1  ; enable bang-bang mode for the bed heater and set PWM limit
M140 H0                                            ; map heated bed to heater 0
M143 H0 S100                                       ; set temperature limit for heater 0 to 100C
M308 S2 P"temp0" Y"thermistor" T100000 B4138       ; configure sensor 1 as thermistor on pin temp0
M950 H2 C"out2" T2                                 ; create nozzle heater output on out1 and map it to sensor 1
M307 H2 R2.962 K0.727:0.000 D8.70 E1.35 S1.00 B0
M307 H2 S240                                       ; set temperature limit for heater 1 to 240C
M308 S1 P"temp1" Y"thermistor" T100000 B4138       ; configure sensor 1 as thermistor on pin temp1
M950 H1 C"out1" T1                                 ; create nozzle heater output on out1 and map it to sensor 1
M307 H1 R80.490 K900:0.0 D20.02 E1.35 S0.05 B0 I0.5 V23.8                                   ; disable bang-bang mode for heater  and set PWM limit
M143 H1 S260                                       ; set temperature limit for heater 1 to 240C

; Fans
M950 F0 C"out9" Q500                               ; create fan 0 on pin out7 and set its frequency
M106 P0 S1 H1 T45                                  ; set fan 0 value. Thermostatic control is turned on
M950 F1 C"out8" Q500                               ; create fan 1 on pin out8 and set its frequency
M106 P1 S1 H1 T45                                  ; set fan 1 value. Thermostatic control is turned on
M950 F2 C"out7" Q500                               ; create fan 1 on pin out8 and set its frequency
M106 P2 S1 H1 T45                                  ; set fan 1 value. Thermostatic control is turned on
M950 F3 C"out4" Q500                               ; create fan 1 on pin out8 and set its frequency
M106 P3 S1 H0 T28:40                                  ; set fan 1 value. Thermostatic control is turned on
M950 F4 C"out5" Q500                               ; create fan 1 on pin out8 and set its frequency
M106 P4 S1 H1 T120                                  ; set fan 1 value. Thermostatic control is turned on

; Tools
M563 P0 D0 H1 F0                                 ; define tool 0
G10 P0 X0 Y0 Z0                                    ; set tool 0 axis offsets
G10 P0 R215 S215                                       ; set initial tool 0 active and standby temperatures to 70C

M563 P1 D1 H2 X3 F1                                    ; define tool 1
G10 P1 X38 Y-4 Z0                                    ; set tool 1 axis offsets
G10 P1 R215 S215                                       ; set initial tool 1 active and standby temperatures to 70C

; Create a tool that prints 2 copies of the object using both carriages
M563 P2 D0:1 H1:2 X0:3 F0:1 ; tool 2 uses both extruders, hot end heaters and fans, and maps X to both X and U
G10 P2 X-70 Y0 U70 S215 R215 ; set tool offsets and temperatures
M567 P2 E1:1 ; set mix ratio 100% on both extruders


; Custom settings are not defined

; Miscellaneous
M911 S10 R11 P"M913 X0 Y0 G91 M83 G1 Z3 E-5 F1000" ; set voltage thresholds and actions to run on power loss

@droftarts
Hi, thank you for your reply. Yes, it is an IDEX machine.
I've applied most of the changes you listed. However, I still have some issues.
First thing is, after applying G98 P"config.g" I receive Warning: G98: Command is not supported

What is more, after changing the offset in

G10 P2 X0 Y0 U0 S215 R215 ; set tool offsets and temperatures

my X carriage, which worked well, is pushing the end of the axis, no matter what value I apply, example used: X50, X70, X100, X-50, always the same (for U axis always opposites of those values), and U still didn't move.
My homeu.g looks like this:

G91               ; relative positioning
G1 H2 Z5 F6000    ; lift Z relative to current position
G1 H1 U665 F1800 ; move quickly to U axis endstop and stop there (first pass)
G1 H2 U-5 F6000    ; go back a few mm
G1 H1 U665 F360  ; move slowly to U axis endstop once more (second pass)
G1 H2 Z-5 F6000   ; lower Z again
G90    

It is after the changes, because thanks to you I finally understood how to calibrate the motors and which way should they work, so i changed

M569 P0.3 S0

into

M569 P0.3 S1

And now, at least I think, the directions of the X and U carriege work as they should.

If you have any idea what can I change or what should I post here please let me know.

Hi,
I've got a problem with the U axis configuration. I've checked the following topic: U axis don't print but couldn't find the right solution for my printer. U axis homes well, but during printing it stays in place or hits the X axis extruder which is waiting in its homing position on the other side of the axis. I cannot get it to print anything. Maybe you wil be able tell me what I did wrong, because I'm on the verge of giving up on the second extruder.

The problem occurs always during printing, no matter if copy or multicolour mode.
My configuration looks like this:

; Drives
M584 X0.2 Y40.0 Z0.0:0.1 E0.5:0.4 U0.3                     ; set drive mapping
M569 P0.2 S1                                       ; physical drive 0.2 goes forwards
M569 P40.0 S1 R0 T5:5:5:5							; physical drive 40.0 goes forwards
M569 P0.1 S0
M569 P0.3 S0
M569 P0.0 S0                                       ; physical drive 0.0 goes forwards
M569 P0.5 S1                                       ; physical drive 0.5 goes forwards
M569 P0.4 S1                                       ; physical drive 0.4 goes forwards
M671 X-20:220 Y0:0 U-20:220 S0.5
M208 X-5:205 Y0:200 U-5:205
M350 X16 Y16 Z16 E16:16 U16 I0                         ; configure microstepping with interpolation
M92 X100.35 Y80.10 Z320.00:320.00 E896.15:896.15 U100.35         ; set steps per mm
M566 X500.00 Y500.00 Z1000.00:60.00 E500.00:500.00 U500.00         ; set maximum instantaneous speed changes (mm/min)
M203 X12000.00 Y12000.00 Z800.00:800.00 E12000.01:12000.01 U12000.00    ; set maximum speeds (mm/min)
M201 X500.00 Y500.00 Z200.00:200.00 E500.01:500.01 U500.00        ; set accelerations (mm/s^2)
M906 X1200 Y3000 Z900:900 E1900:1900 U1200 I30                ; set motor currents (mA) and motor idle factor in per cent
M84 S300000                                            ; Set idle timeout

M572 D0:1 S0.2                  ; set extruder 0, 1 and 2 pressure advance to 0.2 seconds (RepRapFirmware 1.20 and later)

; Axis Limits
M208 X0 Y0 Z0 U0 S1                                  ; set axis minima
M208 X450 Y500 Z475 U450 S0                             ; set axis maxima

; Endstops
M574 X1 S1 P"io0.in"                               ; configure switch-type (e.g. microswitch) endstop for low end on X via pin io0.in
M574 Y1 S1 P"io2.in"                               ; configure switch-type (e.g. microswitch) endstop for low end on Y via pin io2.in
M574 Z2 S1 P"io5.in+io4.in"                               ; configure switch-type (e.g. microswitch) endstop for high end on Z via pin io4.in
M574 U1 S1 P"io3.in"

; Z-Probe
M558 P0 H5 F120 T6000                              ; disable Z probe but set dive height, probe speed and travel speed
M557 X15:215 Y15:195 S20                           ; define mesh grid

; Heaters
M308 S0 P"temp2" Y"thermistor" T100000 B4138       ; configure sensor 0 as thermistor on pin temp2
M950 H0 C"out0" T0                                 ; create bed heater output on out0 and map it to sensor 0
M307 H0 R5.187 K0.400:0.000 D41.47 E1.35 S0.00 B1  ; enable bang-bang mode for the bed heater and set PWM limit
M140 H0                                            ; map heated bed to heater 0
M143 H0 S100                                       ; set temperature limit for heater 0 to 100C
M308 S2 P"temp0" Y"thermistor" T100000 B4138       ; configure sensor 1 as thermistor on pin temp0
M950 H2 C"out2" T2                                 ; create nozzle heater output on out1 and map it to sensor 1
M307 H2 R2.962 K0.727:0.000 D8.70 E1.35 S1.00 B0
M307 H2 S240                                       ; set temperature limit for heater 1 to 240C
M308 S1 P"temp1" Y"thermistor" T100000 B4138       ; configure sensor 1 as thermistor on pin temp1
M950 H1 C"out1" T1                                 ; create nozzle heater output on out1 and map it to sensor 1
M307 H1 R80.490 K900:0.0 D20.02 E1.35 S0.05 B0 I0.5 V23.8                                   ; disable bang-bang mode for heater  and set PWM limit
M143 H1 S260                                       ; set temperature limit for heater 1 to 240C

; Fans
M950 F0 C"out9" Q500                               ; create fan 0 on pin out7 and set its frequency
M106 P0 S1 H1 T45                                  ; set fan 0 value. Thermostatic control is turned on
M950 F1 C"out8" Q500                               ; create fan 1 on pin out8 and set its frequency
M106 P1 S1 H1 T45                                  ; set fan 1 value. Thermostatic control is turned on
M950 F2 C"out7" Q500                               ; create fan 1 on pin out8 and set its frequency
M106 P2 S1 H1 T45                                  ; set fan 1 value. Thermostatic control is turned on
M950 F3 C"out4" Q500                               ; create fan 1 on pin out8 and set its frequency
M106 P3 S1 H0 T28:40                                  ; set fan 1 value. Thermostatic control is turned on
M950 F4 C"out5" Q500                               ; create fan 1 on pin out8 and set its frequency
M106 P4 S1 H1 T120                                  ; set fan 1 value. Thermostatic control is turned on

; Tools
M563 P0 D0 H1 F0                                 ; define tool 0
G10 P0 X0 Y0 Z0                                    ; set tool 0 axis offsets
G10 P0 R215 S215                                       ; set initial tool 0 active and standby temperatures to 70C

M563 P1 D1 H2 X3 F1                                    ; define tool 1
G10 P1 X0 Y0 Z0                                    ; set tool 1 axis offsets
G10 P1 R215 S215                                       ; set initial tool 1 active and standby temperatures to 70C

; Create a tool that prints 2 copies of the object using both carriages
M563 P2 D0:1 H1:2 X0:3 F0:1 ; tool 2 uses both extruders, hot end heaters and fans, and maps X to both X and U
G10 P2 X0 Y0 U0 S215 R215 ; set tool offsets and temperatures
M567 P2 E1:1 ; set mix ratio 100% on both extruders```

; tfree0.g

M83              ; relative extruder movement
M106 S0          ; turn off our print cooling fan
G91              ; relative axis movement
G1 Z5 F500       ; up 3mm
G90              ; absolute axis movement
G1 H2 X10 F6000 ; park the X carriage at -200mm
```
; tpost0.g

M106 R2     ; restore print cooling fan speed
M116 P0     ; wait for tool 0 only to reach operating temperature
M83         ; relative extruder mode


; tfree1.g

M83              ; relative extruder movement
M106 S0          ; turn off our print cooling fan
G91              ; relative axis movement
G1 Z5 F500       ; up 3mm
G90              ; absolute axis movement
G1 H2 U10 F6000 ; park the U carriage at -200mm
M579 

; tpost1.g

M106 R2     ; restore print cooling fan speed
M116 P1     ; wait for tool 1 heaters to reach operating temperature
M83         ; relative extruder movement

; tfree2.g

M83          ; relative extruder movement
M106 S0      ; turn off our print cooling fan
G91          ; relative axis movement
G1 Z5 F500   ; up 5mm
G90          ; absolute axis movement
G28 X U      ; home the X and U carriages

; tpost2.g

M106 R2      ; restore print cooling fan speed
M116 P2      ; wait for tool 2 heaters to reach operating temperature
M83          ; relative extruder movement
M567 P2 E0.5:0.5 ; set tool mix ratio
M568 P2 S1   ; turn on mixing