Picture of Hatches for a skin on frame kayak
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
Rubber mallet

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.