Here's how I did my skerry rails and it would probably work for you.  Use your table saw with or without a dadoe blade bad cut a notch in two of the rail pieces so that when held to the outside of the hull the rails hide the raw plywood edge of the boat.  You can run a couple of screws from inside the boat into that rail to hold it in place while the glue dries.  Next I cut a number of two inch pieces of rail material and spaced them around the inside covering the screws holding the outside rail.  Then I attached the inside rail to those spacers with counter sunk and plugged screws.  You could simplify things and leave out the spacers.  If I had your email I could send you a photo.

Ok, here's a photo of what I'm talking about.

https://www.dropbox.com/s/wtsr9291t37nwna/2013-03-29%2015.02.22.jpg

When I built my cradle boat, I placed the rails outside and even with the top edge of the planking.

I glued the two sections together with slightly thickened epoxy and and also to the top of the top plank at the same time -- clamping with quite a few spring clamps as I went.

Regards,  Mike.

I have built several cradle/table boats.  Several ways to do it as mentioned above.

Since they are not built for the water you have another option I have used.

1. Use Titebond III glue

2.Glue first strip on outside of your top sheer panel.

   Glue makes cleanup and control easy.

3. Repeat on second strip. Once cured you can sand the top edge flush.

Enjoy the build