I believe it is much easier to install both the bulkheads and rudder pedals etc prior to fastening the decks. I used a small diameter plastic tubing through the outside of the boat through the bulkheads for the rudder cables to run through, this enables the cables to be replaced if necessary without removing the deck. The tubing is simply epoxied to the sides using a small piece of fiberglas tape. After installing the deck caulking was used to seal the bottom of the deck and the top of the bulkheads. ( this was done through the cockpit ) I would be a little hesitant about cutting the hatch openings prior to installing the deck as you now have to worry about positioning ( centering ) the decks correctly before gluing. By the way when gluing the deck it is easiest to install using fiberglas stranded tape instead of nails or screws. It is really strong and sticky, just use lots of it to avoid gaps or high spots.

Enjoy building