From what I can gather, they offer 3 choices (hard top, factory soft top, Supertop) because they are fitted in the rear to allow room for the folded up soft top. If you follow this procedure, you can get your soft top to tuck pretty tight into the tub, then the tonneau would strap over the top hiding it below.
http://home.exetel.com.au/jeeps/Removingthetop.htm
The Supertop looks to have a different frame than a factory top, so they must make accommodations for its design. Hard top has nothing back there, so it's a tighter fitting tonneau me thinks.
Yah, I read the "installation instructions" that Quadrtac had for the Bestop I would need. I would have to take the actual soft top off, but can leave the bars. The bars sit on top of the tub hiding under the cover. It looked like I could still use my drawer doing it that way.
In a way, that would probably be my best bet. At least I wouldn't' have to take all the bars off too. I will most likely go with the Bestop for the Supertop. I will just have to wait a little longer for the Windjammer.