Gaz,I always try to avoid the canopy having a "stuck on" look to it.My method,which is by no means standard,is to attach the masked canopy to the model at the end of construction and before painting. This means I can sort out any gaps or other nasties. The masking stays on the canopy throughout the entire painting and varnishing process,only being removed at the very end. It's a bit of a nail biting moment removing it! It's usually okay though sometimes minor blemishes have to be rectified.
Cheers
Steve