You weed (remove) the areas of the plotted mask to be painted before transferring the mask from its backing to the work piece.
This is why I oversize the areas to be painted using the first mask - the carving will actually remove the perimeters of the painted areas, so the colors will be immediately adjacent to the carved areas (which also get painted, before removing the second mask).
Inkscape for all the vector editing. I import my svg’s/dxf’s into Fusion360 for generating G-Code for the X-Carve, and into VinylMaster for the plotter.
I’ve gone through the steps of calibrating both my X-Carve and plotter, so they’re both fairly dimensionally accurate. Again, though, I give myself “wiggle room” so I’m not worried about things matching perfectly.