The Z probe X and Y offsets are measured from the head reference point (which in a single-nozzle printer is always the nozzle) to the probe. So if +X movement moves the nozzle to the right and the probe is to the left of the nozzle, then the X offset will be negative.
If you want mesh compensation to correct for the bed not being flat and level, then it's important that the measured height error is at the specified bed coordinates. So the firmware puts the probe at those coordinates to measure the height error, not the nozzle.
If on the other hand the bed is flat and level but the gantry that carries the print head isn't (for example, in the middle of the X travel the gantry sags a little under the weight of the print head), then you are better off setting the probe X and Y offsets to zero so that the firmware puts the nozzle at the specified XY coordinates.
HTH David