I recently completed a skin on frame kayak and I thought I would show how I added waterproof access hatches to the kayak. This needs to be done before the skin is painted, as it will be too stiff after the paint for the method to really work well.
1 plastic 5Gal bucket $5-10
1 Gamma Seal Lid or similar product $7
thread: the same stuff you used for stitching on your coaming should work. I used 25lb test nylon thread (leftover from stitching the skin)
something to brace the bucket top as you hammer on the lid (I used a scrap plank I had in the garage)
Saw: suitable for cutting the top off a plastic bucket
drill: suitable for drilling holes in plastic
Needle: The same on you used on the coaming should work
The Gamma Seal Lid is a product designed to snap onto the top of a 5 Gallon bucket like a normal bucket lid. The centre of the lid can then be screwed out giving access to the bucket more simply than prying off a normal bucket lid. I found these in the local Home Depot, but they are available online if you are willing to pay for the shipping. Both the snap portion and the screw in-out portion have gaskets and should be watertight, although I wouldn't put my trust in them to be absolutely perfect in that respect.
The basic plan is to saw the top off of the bucket and stitch it into the skin of the kayak. Then we can snap the Gamma Seal Lid on and we have a ready made hatch!
One warning: these lids take a lot of force to get on. I tried compressing them on with my hands, with clamps, and finally with a rubber mallet. My hands were too weak (and I'm a Big guy so I'm not just a weakling). The clamps just deformed the plastic without actually seating the snap on portion of the lid. The mallet was the only thing that worked. Sadly you can't hammer against cloth, so I had to run a brace under the area I was pounding on. My kayak was built using a somewhat unconventional design and had lots of heavy plywood bulkheads for me to use as a platform to run a board for bracing. Read though the whole instructable and assess whether you will be able to properly brace a support for hammering BEFORE you go cutting holes in that nice new skin.
Also, you will want to leave gaps in the seam where the hatch will go, otherwise, you will have to do a little fancy work to keep your seam from unravelling when you cut the hole in the skin. This requires you to have in mind where the hatch will go, before you stitch on the skin. If you didn't leave a gap and you really desperately want to try this, I can only suggest that you cut the stitching thread at the centre of where you want your hatch, then carefully unravel the stitches in each direction and use the loose end to tie off the seam so all your work doesn't unravel.
Step 1: selecting a location
There are two primary considerations beyond simply where you think a hatch would be most useful.
First, you need some relatively heavy pieces of frame nearby to act as bracing for pounding the lid on. If you can insert a board between the skin and your gunwales, you may be able to use a board running from gunwale to gunwale as your support. If you choose to do this you need to recognize that the board will sit above the gunwale, and the bucket top protrudes below the skin surface. Consequently the board will push the bucket top up 1-2 inches. This means you will need to have enough fabric surface to stretch up. If you place the hatch in a narrow area near the front or rear of the kayak, there will not be enough fabric to let the lid rise for this operation. If you can use some of the ribs or bulkheads for bracing this becomes less of an issue
Secondly, the process of stitching in the lid can warp the lid if there is not enough skin to stretch. I put one of my hatches at the extreme rear of the kayak, where there is only 1/4 inch between the gunwales and the hatch. This hatch is deformed, and it is VERY difficult to get the lid to screw in.
As a consequence of these two factors I recommend that you place your hatches towards the centre of your kayak so that there is at least 2-3 inches of clean fabric in all directions around the hatch. Placing the hatch between two heavy ribs or bulkheads also provides a handy support base for hammering on the lids.