I use a flat lip that's shimmed down 1/8" so it will sit flush considering the gasket. My hatch covers are flush cut-outs from the deck.

For gasket material - the self stick weather stripping sold in Home Centers works perfect. I use the 3/8" wide by about 3/16" thick type. Make sure you get the closed cell variety - I think they label it waterproof. Frost King brand is the most common - they make all that window insulation stuff.

I get 100% water tight seals. Part of the watertight success is the use of a clamp down mechanism rather than bungees or straps. You need good downward pressure.