Guess I'm the oddball, then: I always put my canopies on the model and then paint. Here's my sequence:
1. Dip the canopy in Future, let it sit for at least 24 hours (usually 48)
2. Install the canopy on the model (once the rest of the model is complete; i.e. seams, etc).
3. Mask the canopy with either a precut mask (I love these) or using Swanny's method (outlined on his site)
4. Paint the interior canopy color over the entire canopy
5. Prime the entire model
6. Paint all colors
7. Glosscote (Future in my case)
8. Decals
9. Dullcote
10. Remove masking
I've had good results with this so far.