I usually cover all the pices first to get it an ARF.
Much, much easier and cleaner for me.
However, I leave the part the has to be glued uncover.
This way I don't have to go back and try to cut off the film later.

If you run a cut or a line on the surface of the wood, it will
cause structure fialure during flight or the pieces might break if under
force or pressure.

I just put masking tape over film nearest to the glue joint to
protect the film during gluing as madscientist had mentioned

us epoxy for the hinges, unless you're lighting fast.lol

To get trim scheme or design to stick over the base color without a lot of bubbles.
use soap and water and use a credit card or something to sqeezgie the water
out.