I just assebbled my doors 2 weeks ago, so I should be able to help you. There are 2 Vertical tracks, one for each side of the window, one of them has a roller, and one has some kind of delrin slider (or some kind of slippery plastic material). If I remember correctly, the vertical track closer to the front of the car has the slider, and the one closer to the back has the roller.
Depending on which one you took off changes how you put it back together. Either way, I would take of the rubber mouldings on the top of the door off, so you can look down the door and see whats going on. If its the track closer to the front, its fairly simple, just make sure the slider which is attached to the glass is inside the track, and bolt the track back to the door. If it is the track closer to the rear, it going to be a little more difficult..
The only way the roller can get back on the track is from the top of the track. Kind of like desk drawer tracks. If you can, remove that track completely from the door, and roll the window all the way up. Hopefully this will give you enough room inside the door to slide the roller back on to the track. If that doesnt work, your probably going to have to unbolt all the tracks from the door so that the entire window assembly is free to move around inside the door, then hopefully there will be enough room then to slide the track back on.
Good Luck, You may want to get a second set of hands to hold the window while you try to get the tack back on.
Finally got my engine! 1996 teksid bock, cobra crank, manley H-Beam, diamond pistons, 4V b-heads.
Next Steps: Ported 03 cobra heads, Stage 2 blower cams, some form of 15-18 lbs boost---Gonna be a Beast!!!