I rented a jigsaw and cut the hatch openings on the deck. There was also some excess deck on the inside of the cockpit coaming, I removed most of it with a jigsaw and sanded the rest.
I also applied a coat of varnish (Minwax Helmsman Spar Urethane semi-gloss) to the deck
Here is a picture of the hatch openings:
And with the hatch covers in place (they will be held down with straps)