I can only speak from a '69 b-body perspective but you'll probably want to lower the glass in with out the regulator bolted up because to get the regulator roller on the track that is attached to the window you'll need to have the regulator disconnected to do it.

You also might have to install the fuzzies last because you'll need that room when shoving in that window. The fuzzies are a b$#^& to install with the window in but it is doable, I only scratched my paint once