Cut the foam short so there is not a bulge under the top. Another trick from the upholstery guy was to use cotton (not foam as it can collapse over time if not quality foam) in this area to fill in low spots when putting down the top in these areas.
After fiddling I think the best place to start the rear window panel is at the bottom. The Robbins top is a perfect fit to the body line and you can get it centered nicely, then move to the upper side and the window cross bow.