I'm working from memory here, but I think I'm right. I will assume you removed the main door glass when you pulled the vent glass, if you didn't, it will be a real pain to re-install the vent glass straight. They have to go in at the same time and it's real cumbersome and you really need 2 guys to do it.
The rear channel will guide the main glass and it in turn guides the vent glass assembly although the rear main glass channel might have to be loosened to complete the job. It's a trial and error thing and you'll need some patience to get it right.
If I'm all wet on this, somebody please help out. It's been a REAL LONG time.