Joe,
I use masking tape (cut with a metal rule and hobby knife) to mask canopies.
I've tried several different types of liquid masks and I really don't think they work that well for canopies.
Further, if you use the "Mr" brand (it's light blue with an orange cap), it tends to ruin any acrylic finishes - so, if you overcoat your canopies with clear gloss or Future, it'll end up fogging them.
When it comes to painting, if i'm going to leave the canopy open, then i'll paint it off the model and attach at the very end.
If i'm going to close it, then i put it on and paint with the fuselage.
One more point - no matter what, it's much much easier to mask when it's off the model, then attach.
I do, however, use maskol to mask things like wheel wells.
Good luck!