The intake on the bottom probably should be capped off. I'd actually cap off both of the lower returns as well. Whoever drilled the tank went way to far for my taste. I'd use the overflow as the only drain, the overflow return as the only return. That way you'll only need one check valve and you'll have no possibility of water back siphoning out of the tank from the lower drill sites. I'm a BIG believer in making a reef as safe as possible. This is just what I would do.
The guy who drilled the tank must've been concerned, or paranoid, about dead spots behind his rock wall. Unless you plan on having a mountain of rock, going with a single drain and return would be the safest way to plumb the tank. Even if you have loads of rock, one powerhead behind the rock would give plenty of flow in the back.