I went for the two piece, and have never stored it in the trunk. However, i have stored it in the back seats, as others have. its a handy benefit.
Another option, which isn't as fancy is from Haney Motorsport:
Mustang Convertible Soft Tonneau Cover at HaneyMotorsport
Its probably a lot more practical, and would still work with a windscreen:
Mustang Convertible Wind Screen Blocker at HaneyMotorsport Free Shipping!
That is the soft tonneau I am talking about. Does anyone have one? Feedback?