I take the side windows and carefully lay them one on top of the other (inside of the windows touching) in the back of the jeep and then place them flat under the Jeep cargo mat that came with my '12 unlimited to protect them. Been doing that all summer, no issues. I made the mistake of rolling up the back window and strapping it up using the inlcuded elastic bands and while the bands themselves and rolling the window up did no harm, the window rubbed against the metail soft top support on the inside and i have two gnarly scratches up both sides of my rear window so NEVER do that. I came across that rule of thumb too late....so now, i either just unzip and fold down my rear window, or i take it completely out, roll it up carefully, and lay it against the back seat on top of the wheel wells. keeps it nice and secure back there.
2012 Sahara Unlimited
Black Leather, 430N, Dual Tops, Max Tow, 3.73 Gears, Connectivity, Heated Seats, Remote Start, 265/70r18 BF Goodrich KO2s, 18" MB TKOs