CHEAPER BETTER WAY (IMO)
I did a write-up how I store mine.
LINK> Soft-Top Window Storage with Towels and a Sleeping Bag Stuff Sack
I personally like it better with towels than have something all sown together. I can easily roll the windows on my hood on the go. The front bumper tow hooks holds the bag's draw strings so it doesn't blow away. I just pull out the towels as I need them. If you roll them without towels it will create scratches unless they are super clean. With towels I have had no problems with them a bit dusty.
You can roll them tight and they will pop back. I have heard warnings not to ever roll the side that tucks into the door. Folding them is probably pretty safe, but I think rolling puts less stress on the hard plastic. A swim noodle cut to size would be nice for the center, but I haven't done that yet.
WARNING DON'T ROLL THE REAR WINDOW
The rear window was made to be rolled up and attached with a couple straps on the top. If you do that it will scratch up your windows pretty good. You might be able to use a beach towel when rolling to get it to work.