This is a pretty easy fix and has come up here before.
To reinstall the side windows, get the top zipper just started, between 2 and 5 inches. Second is getting the part you are having trouble with into it's groove. That bit of plastic on the front side of the window goes into a vertical groove in the door surround. Many assume that it just gets pushed in as you are probably doing. However, the groove can only be accessed when the door is open, and the front of the window will make a full J hook into it. What you are attempting to push it into is only 50% of the way.
Start at the top and jam it in there. Complete the zipper and then starting at the bottom front, start pushing the bottom plastic flap in. This will fully tension the window. Your problem area can't be inserted when there is much tension at all on the widow. Starting the zipper by a bit just makes the whole thing easier.
Dark out now, but if you need pics I can get them tomorrow at some point.