Something like this perhaps:

http://www.guillemot-kayaks.com/guillemot/tools_and_accessories/recessed_deck_line_fitting

Bri,

Kurt Maurer, who used to hang out on this forum some 10 years ago or so, had a system where he drilled a hole that was slightly smaller than the shock cord diameter. Then he'd stretch the cord and thread it into the hole. When the cord relaxed, it expanded and filled the hole making a watertight pass-through for the cord. The bungees were secured by knots inside the boat.

I never did get that to work, though I have have no doubt that Kurt did. He's that kind of guy, good with his hands. For me, the cord kept shredding and I could never get it through the hole intact.

Instead, I used another of his ideas - threading the bungee cords through webbing loops attached to the boat.

The loops fit through slits in the hull. They are folded-over pieces of nylon webbing. They're stitched in 2 places - once at the end and once in the middle. This forms a figure-8 shaped double loop.

The top loop (unstitched end) is pushed through the slit from the inside so that there is one loop in the boat and one outside. A piece of 1/4" dowel, sharpened at both ends in a pencil sharpener, is slipped through the inner loop. That keeps the loop from sliding out of the boat. The bungee cord is threaded through the outer loop and keeps the loop from sliding into the boat. The pressure between the hull and dowel squeezes the webbing into the slit where it acts as a water barrier, mostly sealing the slit.

The attachment is soft, so it doesn't unduly strain the boat by concentrating forces. It's strong enough to let you pick up the boat using just the bungees. It can be completely removed with no tools in a matter of seconds for cleaning and repairs (though putting it back takes a few minutes). The only downside is that it is not completely waterproof. While the webbing prevents large amounts of water from coming in, a full day of paddling in rough water will let in a cup or so of water.

But hey, kayaking is a water sport, right? You'll get that much water through a spray skirt, dripping off the paddles, splashing over the coaming, etc., so what's a bit more?

Have fun,

Laszlo