I agree with GM, getting a good fit of the canopy early is the best way to take care of the gaps. I've had white putty leak in too many times before that lesson sunk in! For desperate times, I've used black Apoxie Sculpt, if any squeezes under the canopy it is less likely to be noticed.
Tamiya tape works great for 1/48 and above scale, ok for 1/72, and not so well with 1/144. For the smaller scales, Bare Metal Foil works better. I just did a 1/144 Bf109 canopy with Bare Metal Foil, it would have been very difficult with tape.
Bare Metal Foil becomes harder to remove the longer you leave it on, so you'll want to finish your painting withing 2-3 days. After you remove the foil mask, any adhesive residue comes off with Goo Gone or WD40.
Sometimes I use Future, sometimes I don't. If you can't find future Mop-N-Glo works just as well. Scrape the paint from your attachment points and the glue will stick better. Aileen's Craft glue works very well.
Sometimes canopy framing detail is a bit mushy and it's hard to place your masking material. Just cut a strip of tape the width of the framing and place it where the framing should be. Place your masking material as you normally would and cut around the tape "framing". Remove the tape framing and paint.
And finally, canopy masking is much easier with an optivisor and the right light. The light should allow you to see the framing either by shining through the tape, and/or creating a shadow line. Use a toothpick to burnish down to the line, then a new, SHARP blade to make your cut. A dull blade just drags the tape or tears the foil. Apply just enough pressure to make the cut, no more.
Practice, practice, patience, you'll get it!