Here are some pictures of how I attach my hatch covers from the inside.

The top photo shows the 4 "hooks" that are carved out of maple and epoxied to the hatch cover. The "hooks" are placed so that when the bungee cord is hooked in place the pressure is spread evenly across the hatch cover.

The bottom photo shows one of the two blocks that are mounted on the inside of the boat along the shear line. The other block is on the opposite side of the boat. The bungee cord stretches across the boat from shear line to shear line in 2 places. When the cover is off the bungee is actually very loose, which is why it looks like it is running down along the bottom of the boat in the picture.

To attach the cover I place the far side of the hatch cover on the hatch support ledge. I then pull each bungee up and connect it to the appropriate 2 "hooks" on the cover. This provides more downward pressure than can be achieved with deck mounted bungees.

There is a finger notch visible (blurry) in the bottom photo which enables me to get my finger in, lift the cover up, and then slip the bungees off the hooks for removal.

I haven't had a chance to test how watertight the seal is, but it should be at least as good as the flush hatches with the bungees on the outside.