>>After you've mounted the negative and taped down the mylar, do you then lay the Creo film mask over everything?
Yes

>>how do you keep things registered.
The mask opening should be a bit larger than the film size. Then use strips cut from opaque material or another old mask to perfectly cover the edges from light spills. Carefully and slowly close the lid so the strips don't move. Or just gently tape them in place to the main mask.