I tried that a few times when I first got the tent, but I just decided to remove the fly altogether because it's one less hassle to deal with. I'm in CA where were in the middle of a 4 year drought, so any rain that happens would barely get the fabric wet. Most of the time I just rely on the fabric panels to cover it because I love opening those windows first thing in the morning. I'll probably put it back on (or at least keep it in the car) when I go to the sierras in a couple weeks.
There is velcro surrounding those roof windows and on the Tepui website it mentions a "clear window accessory", but I don't think I've ever seen a picture of it. While I think it might be cool to have clear window on top, I don't know how great it work for stargazing though a wrinkled piece of plastic, and I would be worried about the longevity of it. Every convertible jeep window I've seen looks like crap after a while.