You want to remove the protective film at the very last moment, literally just before sealing up the device, otherwise you will probably have fingerprints and other smudges on the glass surface.
In order to put the Home Button flex in place, you can just lift up the bottom edge of the protective film, apply the flex and then put the film back in place.
Check out this answer ([post|547310]) I posted earlier for other general best practices on the iPad Air/5 re-assembly.