Hi, Spitfire- I also try to attach at the last of the build, especially if it's one color. If camo pattern extends into the canopy, (they almost all do,) it pretty much has to be painted on the fuselage. In which case I do my filling with strip stock, sanding and fitting in stages, not difficult, maybe a bit more time compared to filler from tube. When fuselage is ready for base coat I mask inside and leave canopy off, then spray. That base is sprayed on the canopy, while off the fuselage.
Then, to spray the camo patterns I temporarily attach the canopy with a variety of canopy adhesives, Testors, Future, even white glue, which actually does a pretty decent job of holding it in place, on a temporary basis. After spraying the camo pattern, the canopy can then quite easily be removed with very little force applied, clear coats can be applied to masked fuselage, canopy again spayed with clear coat off the fuselage.
Any mishaps like mask leaks, or any other flubs, can be addressed and remedied with the fuselage and canopy as separate units. When model is completed I attach canopy with those mentioned adhesives, even after the model has been completed for months, dust and just crud can find it's way into the inside of the canopy, there to reside forever and infuriate me. The less aggressive adhesive allows me to gently just pop the canopy off and clean, then re-attach.
Might sound an odd system, but it's worked well for me for quite some time. Cheers.
Patrick