[65Bowrider]

Rockdoc,
The innerliner was a sealed-air-tight compartment to the hull. There should have been two scupper holes in the aft cockpit corners with drain tubes that crossed to the opposite sides for draining. This was for the protection in case one side of the transome got caught under a dock. Originally there were flappers on these drains. Under the engine cover, the liner had about a 6" raised lip, to keep 'washdown' from running into the bilge area.

Do you still have the original inner liner? or has the flooring been replaced?

Seeing some pictures of your inside transome area will be good too.