All soft tops are designed to do that with them. Just unhook the front and fold everything to the back. Some companies have a cover that you can install over the top when its down to keep dust and debris out of it. It's called a top boot.
Mine had elastic straps that you used once it was down, to stretch over the bars and hook into the side channel so that everything didn't rattle. That was a Bestop.
'87 YJ, 4.2L built and bored, 8.5" of lift, 8.8 rear, AX15/NP 231, Tom Woods drive shafts, Flat fenders, 12,000LB winch, Custom bumpers, Rattle can paint job. Never completed...