Thanks for the input guys.
Right now I think the batteries (3 of em) are connected in parallel. One battery is under the hood and two of them are on the passenger side and towards the back of the van.
A plan is to use a cranking battery under the hood, and then two deep cycles on the side. Then put a relay (like a glow-plug relay- GPR) to isolate the cranking battery from the deep cycles. Basically, turn they key forward and the relay will click ON - connecting the cranking battery to the starting batteries. Turn the key backwards and the relay stays Off which means the vehicle is relying only on the deep cycles (the two on the side).
But what (voltage) on an average vehicle is Off when the key is turned backwards and On when the key is turned forwards (like to start the engine)?