Glass the outside of the deck next. Whatever you do from here on, it will be easier and cleaner with the outside glassed. You can clean up epoxy, you won't stain the bare wood, and you'll be able to do you coaming and / or recess cleaner. Plus you'll be able to handle the glass fabric easier rather than trying to glass a hull of an attached deck.

If you get any epoxy drips or stains on bare wood, it's a major problem.