The roll-up method probably will not work with the JL top having a more rigid c-channel guide, no zippers. Get a Mopar soft top window storage bag.With the JK it was very common to remove the rear window form the rear window bow and then roll the window in a soft towel with a cut down pool noodle in the center to keep the roll round. Window bow went back into its spot on the Jeep. I don’t have my JL yet but I don’t know why that wouldn’t work.
I had a towel and piece of pool noodle in a sleeping bag pouch so I could get it contained in the back. The side windows used to fit in there too but now with the molded corners I doubt it would.