Marc,
I deal with windscreens, & glass parts that need to be attached prior to painting, verses canopies and glass that I can attach after paint differently.
All glass is masked with either bought masks, or using Tamiya tape in various ways. Windscreens, etc. that need to be glued prior to painting are dry fitted till the best fit possible is attained. I carefully use Tamiya Extra thin around the joint. I've never had any fogging nor glue stain issues as I can control where, how, and the amount of glue. Once dry I can blend the parts in with various methods/products.
For parts that have been painted off the model, and the model has painted and sealed, I prefer to use Aleene's Tacky Glue as it's a much stronger bonding agent then regular White glue, and seems to tack up and dry quicker. The glue does stick to paint and every clear coat I've used, so you can paint those areas without any issues later.
Joel