I think I would cut out the oval shape out of the glass around the cockpit areas before starting(i.e. do not try to tackle glassing the vertical part of the cockpit now) . The cloth shifts around a lot while working the epoxy into the weave, you will need to smooth the cloth out with a brush before starting. I think i would start at the middle and work out if I was in your situation.

Be sure to carve a time slot out to do both sides in a timely manner and not let them sit around and warp and harden off into that shape. This will pay out when mating the deck and hull. Having already done the cockpit will work in your favor in this regard.