The vinyl is made in two pieces- one for the big panel and a separate piece for the bubble. No need to cut the vinyl, only the thin fiberglas. And a common fine-tooth wood saw works well- no need for a hacksaw. The nuts and stud-strips need to come off and the vinyl pushed away a bit from where you're going to saw.
On cutting the top of the bubble, try to visualize what the bubble will look like after its separated from the main cover. I think I cut as close to the actual bubble-edge as possible while not scraping its vinyl, not close to the padded roll. After you're all done, use a few spots of glue to hold loose vinyl edges wrapped around the new cut edges. Any bare fiberglas edges can be touched up with a black Magic Marker to become invisible.