I am looking at my canopy -Veco Hurricane-- and am wondering if I really want to glue it down before painting the plane.
The super-zoot way to do this is to finish out the cockpit area to a bit past the canopy. Do it up really nice, because you'll be gluing a canopy over it.
Then get every speck of balsa dust out of your shop, clean the cockpit and the canopy thoroughly, and glue on the canopy.
Then finish the rest of the plane, including about 1/8" or so up the canopy.
I haven't done this for a good long time, and I'm freaked out that I'll end up with balsa dust all over the inside -- whatever you seal inside there stays, and balsa dust shows up a lot better at the field than in your shop, for some reason.
Alternately, paint over the canopy. You could even make a canopy out of a balsa block. You see lots of stunters done that way.