Since the soft sides won't be on the Jeep all the time, I sewed storage bags for them. I sewed two bags - one is for the attachment components - the c-pillars and the zipper strips and their retainers. It's got separate pockets to make it easy to keep similar-looking left and right parts separate and to keep the painted c-pillars from getting scratched.
The second bag is for the soft side panels themselves. Unlike the first bag, which is primarily used for storage of the components when the soft sides aren't in use (like during the winter when the hard sides are in use), this bag will be carried in the Jeep for times when rather than rolling the side panels up and leaving them on the Jeep, I'll just unzip them and store them inside. This bag also includes a fabric sheet that goes between the two side panels as they're rolled up, it will prevent any scratching, and for convenience in rolling up the two panels it's got velcro on it to attach to the velcro that's already on the panels. This one has a drawstring closure; the other bag has velcro closures.
Since it's winter now, the soft sides will live in these two bags for the next several months.