You have side windows in your hood? My car now has a Simmonds easy-up conversion, done many years ago, but I remember the struggle to fold the hood when it was a 9-stud pattern. One needed to take care when folding sides-to-middle that the fold was outside the seam at the outer edge of the rear window. But it didn't have rear-threequarter windows, just a monster blind spot between the trailing edge of the rear sidescreen and the corner of the car.
Looking at images online it seems that some hoods did indeed have window panels in the back quarter. Maybe that was another poverty option not taken on my car! I would guess it's possible to make the first folds (folding the side bits into the middle to make the whole thing more rectangular) in such a way that you don't crease either the back window or the side panels, but that they end up on top of each other, and you fold the rest up around them, if you see what i mean. There's got to be somebody on here who has one of these strange beasties and knows how to do it!