AM3R1CN-
This reply is just a "heads up"....
Recently, we had a lot off people on here who were, well, un-helpful. You can read about that
here. (also stickied at the top of this forum) Comment's such as your last might rub those in power the wrong way.
However, it goes without saying in any forum, that the search function is your friend (especially when your post count is less than 5)
We're a friendly community, I promise. Some of us are seasoned vets, and some are still noobies. Just get to know us before you start telling us where to shove it. You'll get more help that way.
To answer your question, I've never seen it done that way when homemade, but there are plenty of us who use the OEX bait tanks, or even made them ourselves (myself included). It would be an interesting idea to use the scupper holes, and it might look pretty clean. Just make sure you measure twice, cut once- and with a little luck it'l look great. As for the inner workings, the one way valves might be a little tricky. Honestly, I don't think you need to reinvent the wheel on this. It sounds like you'd spend a lot of time and effort on building something that can be done much easier and cheaper with a much more common set of plans.
Either way, best of luck to you, and I hope it turns out good. Keep us posted.