I leave my canopy off until I'm finished painting/washing/decaling whatever. It is the last piece I glue on.
What I do is take some tamiya masking tape and cover the cockpit opening. Then I take a new #11 blade and cut along the canopy rails so that the cockpit is covered but the tape doesn't interfere with painting.
This way, I am absolutely guaranteed to not get stray paint/primer/gloss/matte on or under the canopy. After I dip the canopy in future, mask it, dip it, paint it and dip it one last time, I leave it in it's drying container until I'm ready to attach it to the plane. At that point, I remove the tape from the cockpit (which comes off no problem as the contact area was so small) and use watch crystal glue to attach the finished canopy to the finished model.
-Fred