If you look at Swanny's tutorial on using Alclad II....
http://www.swannysmodels.com/Alclad.html
...he masks his canopies, then primes them with the same primer he uses for the rest of the mode, Krylon gloss black. This ensures that the canopy frames match the rest of the model.
Also, Swanny specifically points out that he has never had Alclad lift when using masking tape when he's used the proper primer; with the Krylon gloss black primer, this is not a problem. It can be a problem with acrylic primers.
I have yet to go wrong by following Swanny's advice.
On Bench: AM P-51B, Tamiya 1/48 F4U-1A
On Deck: Hasegawa F-14's (too many); Tamiya P-47D; Academy P-47N;