Tuck in the quarter-lights (you can see one of the cords that pulls the rear bar into the correct position when the hood is erected).

Lower it into the tonneau space, holding up the rear edge to lift the rear bar and stop it jamming on the wheel arches.

Lay the rear part over the rest of the assembly. The folds should all be in the material not the windows, and the strips between the rear window and quarter-lights should be lying over the header rail clips.

This picture was taken to show the windstop, but also shows how flat the tonneau cover is over the hood, which has dropped down completely into the space behind the seats.

65 with the later Michelotti frame all the way, as well as still being fastened to the rear panel. It has the rear window zipped out though, so maybe that makes a difference.