I'm not sure if this applies to your particular configuration, but I was preparring to edge glue a canopy to the top of a Monokoted Kaos, when someone else told me the best way to do it:

Take the unglued, trimmed canopy, hold it over a piece of 3/16" balsa sheet, draw around the canopy on the balsa, cut out the balsa and sand it so that it fits nicely up in the canopy so that the edge of the canopy is flush with the bottom edge of the balsa.

Now Monokote the balsa with a color to match or contrast with the top of the model, glue your pilot to the top of the MKed balsa (maybe even run a piece of 1/4" dowel up thru the bottom of the MKed balsa and glued into the pilot to make sure he doesn't later decide to "move about the cabin"), put silicone rubber around the edge of the MKed balsa and place your canopy over your pilot and let dry (put plastic under the balsa so you don't silicone the MKed balsa to your workbench.

Now you have a canopy/pilot fixture with goobs of surface area you can silicone glue to the plane. If you want to take the canopy/pilot fixture off to recover or reposition, just slice it off with some dental floss!

Howzat,
Joel