The windows are the part you really want to store carefully. Suggestions for that range from rolling them with a blanket, storing flat under the bed, etc. Someone (can't remember who, sorry) suggested using those hangers with the little clips on them. i thought that was a clever idea. And, of course, we sell a product designed to keep your windows safe (and you can never go wrong buying more and more of our stuff!).
With the top itself, it doesn't really matter if you roll it, fold it, etc. You just mostly want to avoid the "back of the garage" problem where stuff gets tossed on top of it. A heavy box sitting on the fabric for a few months won't do it any favors.
Oh, and you should take the time to clean it all before you store it. Soapy water and a soft brush on the fabric, a clean soft cloth for the windows (no papertowels on the "glass"). We sell cleaning supplies as well - and you can never go wrong buying more and more of our stuff (but soapy water will work just fine).