I can get the boot open, and the top goes up, but the back part with the window will not pass the lip, or even come up a bit. I know the roof works because I bought it with the roof up, and the guy I bought it from put it down. From what I can understand you have to put the roof up, but not latch it at the front, and then fold up the rear window perpendicular to the ground, place back the boot lid, and then snap down the rear window of the softop.
There must be a trick to this, as I cannot figure out the mechanics of it.