For a battery box if you have anyone around your area that has any military vehicles look for the Dodge 880 series they have a very nice wide box that fit's in the stock location the military truck's come with a very wide battery and most also have 24 volt system's so they had a battery box on both sides of the frontend

 

I use a 70 amp relay to the Deep cycle battery. Relay is driven by logic when ignition is on and starter is not engaged. Ignition AND Auxiliary works.

Ignition + goes to one side of the 70 amp relay coil. The other side is grounded by a pilot relay driven by the switched auxiliary.

Then it's a no brainer. When it's running, the Deep cycle is charging. When it's not, even if the key is in the auxiliary position, it is isolated.