Haven't had to store the soft top....yet, but probably will over this coming Winter. It came installed from the factory with a canvas wrap/bag thing that we'll try and put back on before packing it neatly away in a spare bedroom (read: putting it on the top of a massive pile of stuff in our junk room).
I'll be making sure it's nicely wrapped up though - there are a large number of deadly spiders in my area which love to create huge web networks in this kind of thing. We were in the middle of putting the back seat in the Jeep after it sat for a week in the garage and I noticed one of these
had made a home in the middle of it.