If you're wanting the water to go overboard, like a TRUE self-bailing deck, then, you have to build the inner deck where it's about 2 inches higher than the waterline of the boat, and use some scuppers.
To send the water to the bilge, any height deck will work, you just have to cut a drain in the center of the rear-most part of the deck, for the water to drain through and go to the bilge.
Another option is to have a sump on the main deck. You do this when the inner deck isn't high enough to send the water overboard, but you also don't want it going into the bilge. Water in the bilge won't hurt an outboard, but with an inboard boat like mine, you want to keep as much water out of the bilge as possible. To create the sump, you need to make sure to seal up around the rear rib where the deck ends. This means putting some 5200 under the rib in each gutter, so water going into the sump stays there, instead of running into the bilge. Cut a 4 or 6 inch diameter hole in the inner hull, and install a round hatch plate. Then, in your sump, you install an automatic bilge pump. The auto bilge pump eliminates the need for a bulky mechanical float switch, as the space in the sump is at a premium. You'll also need some type of cover with a screen to keep trash out of the sump.
The inner deck will consist of the floor panel, and the 2 side panels, which will be put together by welding, or, if by some miracle you can find a sheet of aluminum large enough, you could make it a one-piece panel, bending the left and right corners with a metal brake. Place closed-cell foam between each rib, along the bottom, as well as between each rib along the gunwales of the boat, and then rivet the panel to each rib.
Check out the photos on my aluma-jet thread to see how I built the inner hull for mine.