I almost always use PVA (poly vinyl acetate) wood glue for canopies as it dries clear, thins with water, and it's easy to remove excess glue from the model. Just use a dampened Q-tip.
For canopies that fit really well, I use Future as an adhesive. It also dries clear and is easy to apply.
I also use liquid glue like Humbrol Luquid Poly. If you're careful with the stuff, you shouldn't have any problems with it. Just don't let it go where you don't want it, or it'll kill your clear parts.Cheers
LeeTree