This may sound a little complicated-and it does repeat some of what has been said.
1.) Hold the back top edge a little above window opening and press the velcro in place just to hold it up-it is like using the velcro as an extra hand.
2.) Start the zipper on the front of the window and only move it about 6-8 inches.
3.) Tuck in door surrounds and belt rail, which will secure the front and bottom of the window. (don't worry if velcro comes loose now.)
4.) Complete the closing of the zipper-and smooth the velcro into place around the rest of the window.
This method worked best for me when I used the factory soft top. One of the reasons is the very last step when installing the soft top, was to close the front latches on the header. That way the material for the back windows will "move around" more. This includes the very back window-when the latches in front are finally closed, everything is than pulled tight. Hope this helps.