I took my soft top off yesterday and cleaned the windows and placed them in a storage bag from Quadratec after they dried. They're hanging in my basement.
I plan on going to Home Depot or Lowe's today and getting two shelf brackets and covering them with pipe insulation, mounting them 48" apart.
I'll fold the top up like you would while it's mounted on the jeep and hang it for the winter.

 

I bought a rug storage bag from UHaul...$2.95. I cut the closed end off, slid it over the folded soft top/frame, and wrapped it with bungie cords. It will stay dry, clean, and protected. It's hanging in my garage, which is heated all winter. Otherwise, I think I'd bring it inside.