I'll take some pics next time I'm at the boat. For the forward hatch, I cut the flooring to fit the existing plywood hatch. The transmission access hatches are contained within the bunks - remove the bunk top, then remove the hatch.
For flooring, I would only go with engineered flooring. This is the type that is essentially plywood, NOT MDF. MDF is like a sponge, and will swell in a humid environment (i.e. "a boat"). I would also not use solid wood as it will move too much. I toe-nailed mine down, but you could also float it. I would not glue it, as the flooring needs to move with the humidity. Mine has been down for a couple of years and gets lots of wear and water from the kids. So far, it's doing great. Only drawback I see is it is very slippery when wet. The floor had carpet when I bought it, and I just couldn't imagine that wearing well with kids, sand, mud and water.
FWIW, I went with Brazilian Cherry from a closeout sale at Home Depot. Regular price was about $9/sq ft and I got it for $3/ft. The prefinish on this stuff is incredibly tough, but it makes the wood look a bit plastic.