@mihaitintea
With the setup you describe you don't need to edit config.g between each change. I would setup one of the extruders as tool 0 and the other as tool 1 and then just select T0 or T1 as you need.
I think cura can be configurered with multiple tools, and then just select 1 specific tool for the whole print, depending which hotend you want to use.
Define the tools as shown here: https://duet3d.dozuki.com/Wiki/Gcode#Section_M563_Define_or_remove_a_tool
You should be able to connect the smart effect to the E0 or E1 endstop and configure it as a simple switch, however you will then not be able to update the sensitivity of the smart effector. it is unlikely you will need to do this, and if you do you can set it using the z probe port and then swap back to the endstop. Think of the smart effector connected to the endstop as a simple switch: https://duet3d.dozuki.com/Wiki/Connecting_a_Z_probe#Section_Microswitch
the only bit that will require a bit of customising is using a different Z probe for each tool. Possibly setup a macro to sun the Z probe setup lines you would notmally have in config.g for the other tool as part of your manual tool change.