If the tracks are of the soft vinyl type, set the wheels how you want them, just make sure they are in line, front to back, if you follow my gist.
AS for the painting bit, as others have said, build up as much as you can and paint in one go, just be extra careful with gaps between things and under things.
I built my Challenger up into sub assemblies and painted them, I actually followed the instructions this time!!! (first time for every thing).... There are a few bits that will need touching in after the few small extra bits are in place, but that's pretty much the norm.
Ian M