Easiest way is to mask off the pit opening with tape or foam, and install the canopy pieces after. Engine opening can be masked with a piece of soft foam or tape.
To paint the canopy framework, easist way is to mask off the glass panes and paint all the frames in one direction (ie. all the horizontal bars), let dry and then do the other direction (ie. all the vetical bars). This was from another member here.
Paint on the outside, but first color should be the interior color, followed by the exterior color.
Give the entire thing a coat of gloss clear prior to decals, and another light glosss coat after decals are dry. You can then do whatever weathering you want, and a final seal of dull clear. Then install the canopies.