To do the wiring in a box like that... You'd do two separate series battery sleds... You'd end up with two positive and two negative leads... You'd bridge the positives together. And bridge the negatives together. That leaves you with one positive lead and one negative lead. It's as per the usual at that point. BUT, you may want to consider adding addition safety precautions, ie: resettable fuses on both positive leads before the bridging, parallel mosfets, and maybe a killswitch.
Edit: Didn't realize this thread was as old as it is. Either way, the information is accurate enough for anyone else to use, so there's that, I guess..