On my two door jk I just put my soft top on to get ready for the spring here in nj and the side windows do not tuck flush with the door on the top; they stick out when I shut the door. Is this normal or am I doing something wrong

 

Are you talking about the part right behind the door that run vertical?

 

Yeah that part

 

Funny how many people I found asking that question when I myself looked for the answer a few years back. I believe there is a write up somewhere or I you tubed it or something but basically its a technique. Obviously one nobody that ever rents a Jeep in Hawaii knows as those ones are always jacked up when we get one.
Any way, you start the window by zipping just about 2 inches at the top, then start the channel at the bottom about 2 inches. This sort of lines it up. Don't zip or fasten anymore than a couple of inches. Next, stretch the whole length forward (the vertical plastic piece) and sort of roll it into the channel it tucks up inside a groove. Once you see it you will have sort of a duh moment. If my explanation isn't good enough, I can try and find the pictures I saw. Once that is tucked in, zip the rest, then finish tucking the bottom part. You will become a master at it eventually as you will take these on and off all the time.
Hope this helps.