If you want to make a flush hatch I would true up the inside of the opening with files and sandpaper to the shape you want. Then cover the edges with several layers of masking tape followed by a layer of packing tape. Tape the hatch cover into the hole from underneath the deck with packing tape in precisly the position you want the finished hatch cover. Thicken some epoxy with microballons and some cabosil and load it into a syringe. http://www.clcboats.com/shop/products/boat-building-supplies-epoxy-fiberglass-plywood/marine-epoxy-fiberglass/epoxy-syringe.html Then slowly inject it into the gap between cover and hole. Use a slow hardner and temps below 70 degrees F, because you will need some time to do all of this while working with a syringe that has a thick plug of resin in it. Clean up the excess with a clean putty knife or sharpened tongue depressor, followed by some solvent.

I like West System phenolic microballons because they are lightweight, easily sanded and come in a red-brown color. The color changes and becomes a bit darker and more saturated when added to resin. However, if you have a wont for dookie schmutze you will find that even the lightest colored woods change to very dark brown when added to epoxy resin. I like cabosil because it is white in color and makes the resin much tougher and stronger and also makes the resin very difficult to sand.