On a 4 door make sure you do not mix up the front and rear bows, you will either bend a bow or break a door surround if you do. After the canopy is on, back window goes in first but don't secure the bottom until everything else is on. To get windows into channel rails start the zippers about 1 or 2 inches on both the side and the back. Get side channels in then zip in windows. Use the rear window to adjust side to side if the side windows aren't tight when you are lining everything up.
It seems kinda complicated but its really not. Just take your time the first time and know that you likely won't be able to fully zip all of the zippers until about a month later. The fit is really tight, as it should be. Also, as mentioned before, sun helps greatly.