I’m trying to figure this out…
Should I prime all the parts while they are on the trees?
Should I wait for the parts to be assembled and puttied before I prime the wings and fuselage?
The canopy needs to be puttied to fit correctly, so should I attach and putty the canopy before I paint it?
How do I keep from painting the wheel wells when I’m painting the underside of the wings?
Any help would be appreciated 
I have never painted anything on the tree. There is usually mold lines, flash, pinholes and many other thing to be filled or filed off that most of the paint would be gone.
Some parts can be painted with primer and the top coat while still on the tree. After removing, just touch up the area that needs it. Large parts should be attatched to the aircraft, seams filled and sanded prior to painting.
Install the canopy, putty where needed, sand, polish, mask and then paint.
Wheel wells, speed brake wells and any area you don’t want to paint should be covered. One way is to use low tack tape and apply over the area. Using a new sharp # 11 blade, carefully cut around the contour of the wheel well, leaving the tape over the wheel well. This will cut down on most of the paint entering the wheel well. You might have to do a little touch up with a brush.
Another way is to tack glue the wheel well covers in place and remove them after painting. l
there’re numbers of ways to do that…mostly what berny and umax said are correct…however i would like to add something
for the underside thing…i used 2 method…
RE: Painting wheel wells.
I’ve always had better luck painting wheel wells and speed brake wells after painting the rest of the model. Just mask off the area around the well and shoot. At the same time, shoot the inside portion of the gear doors and speed brakes. Be sure to make the outside portion of the doors/brakes if you’ve already painted them.
Rich