The solution was already posted, but I can understand how it is difficult to see.Glad I searched before I posted the exact same question about the Supertop NX. However I am making sure that I get the square edge tucked around the door surround. When I try to close the door, the air being pushed in front of the door edge blows the edge of the window out, so it isn't tucked properly when the door shuts. To combat that, I held the edge of the window down, and pressed the door up against it and then just gave the door a shove to make it latch. The window seemed to be sealed properly, but after a 15 mile drive, with speeds of no more than 60 mph, both sides came out and started flapping.
Is there something else I can do to make sure the windows stay tucked in the doors? My pictures look exactly like the OPs.
The solution was already posted, but I can understand how it is difficult to see.
If you open the door, look closely at the door surround where you are trying to wrap the window around it. Hopefully you'll notice a slot in the door surround, running right along the edge of your window panel. You need to pull the window closer to the door surround and press the window into that slot, kind of similar to how the bottom of the window attaches to the body of the jeep.
A lot of people miss this when putting on a soft top, I did this a few days ago.