I virtually never take the things off, but I had to remove them and slide the top back to install a Rock Hard 4x4 cage. Without going off on a tangent here, the bars for the cage were too short and pulled the factory overhead bars out of alignment. There are little indexing holes in those bars that correspond to some plastic posts on the underside of each Freedom Top panel. The pins drop in those holes, etc. I learned there are adjustment bolts for the side bars, accessible through the upper of two holes in the plastic trim pieces at the upper corners of the windshield frame. They are usually rather loose. Tighten them to pull the bars outward, loosen to let the bars float inward a bit. When you get them right you should be able to drop the little plastic guide at the outer front edge of the top panel into the slot in the weatherstrip and have the panel drop into place. If they are aligned right the gaps should be relatively even in front, rear and down the center. TRICKY to get right.
Back to my Rock Hard 4x4 cage install, the over head bar bent the side bars inward and the adjuster bolts wouldn't correct the misalignment. To get the tops to fit right I had to slot one of those indexing holes enough to allow the top to center.
Driver has no money. Owns two Jeeps.