I did mine the same way for the front deck. I don't mind if a little water gets in there because it's it my seating area anyway, not in a bulkhead area.

I got the bungie to go through by using a trick that someone else here described at some point. I clamped the end of the bungie to the table and then pulled the the bungie taunt and clamped it up about 4 inches from the first clamp. When the cord is stretched, it gets pretty thin. I then use some super glue and a little accelerator. You really don't need the accelerator, it just makes it go faster and I can be impatient. Once the glue is set, I release the clamps,the area that you glued stays stretched and thin. You then cut off the end with the inch or so that was under the clamp and didn't get glued. Voila, you have a thin leader to thread through the holes. It only takes a couple of minutes, but it works great.