MacGuyver is correct, however, when I installed my new BesTop soft top there was NO way the window fronts were going to rotate into the jamb once you fastened the zipper. It was like the zipper location on the top was sewn a bit too far back and there just was not enough material to stretch the edge of the window forward enough for it to fit. In my case, the top was new and not yet stretched out, so that was part of the problem, but we are only talking about stretching the material over about less than a foot of distance (zipper location to door surround) so that was not the whole answer. I already had the rear bow as far forward as it would go (the furthest forward adjusting hole). In the end, I actually shortened each leg of the rear bow 3/4" with a hacksaw, and I was able to get the window to fit...and the top is still very tight. (Plus, I have a lot of adjustment left if needed later). Even so, it's hard to make the window seat properly at the top when installing it. If it were easy, I would remove the zipper and resew it with the mating end about an inch further toward the window, or somehow add 1/2 of material to the front of the window.
In the meantime, you can try unfastening the rear corners of the top, and with the frontbow fastened to the windshield, install the front edge of the windows and get them seated well. Then pull down and refasten the rear of the top, then finish zipping in the windows.