I actually work in the opposite direction...
I'll paint the underside colors first, including the wheel wells. Once it's dry and gotten a gloss coat (usually Future), I'll cut a piece of Glad Press n' Seal and put it down over the wing, making sure there's a fair amount of tension over the wheelwell area. Then, with a new No. 11 blade, I'll cut the opening for the wheelwell and spray the color.
I've never had any bad results...
Jeff