Hey there Dan,
Check out the painting forum, I believe they already have a thread on masking there.
When painting the canopy spray on a coat of interior green first, followed by black, and finally the body color. This should prevent light from passing through the transparencies and give the frame a solid appearance and thus blend well with the rest of the airframe.
There are several methods of mounting clear parts. The safest for me would be to use white glue. But for winscreens especially, I mask the part first, spray the outside with the interior color, attach it with superglue (but be careful, too much and the interior will fog), putty the seams (where necessary), and spray paint as described above).
Hope this helps.