This is an FSB, not an FSJ, but it's the concept I'm thinking of. The tray is three point mounted with SRE's because that chassis is a C-Channel and the degree of flexing is/was an unknown. I didn't want to build it rigid only to have the chassis flex tear it apart. For those not familiar with FSB's this is directly under the pass side rear seat. Both batteries in this truck are Group 65's, they're not small.
As far as the wring is concerned, it need not be all that big of a deal. Use a
marine two post isolated stud in the engine bay near where the battery was and where the existing cables will reach. All of those connections remain the same, they're just going to the studs instead of the battery directly. Then bring both power and ground cables, of the same size(!), from the battery to the isolated studs. DO NOT simply ground to the frame back near the battery. Bring the ground from the battery up to the stock location or to a stud. Anyone who's built a drag racer, moved the battery to the trunk, and found that it cranked slow will understand why you want both power and ground cables. The frame has enough resistance at high currents to making starting, particularly hot starts, a problem.
Alternately you can use a marine battery switch instead of the isolated studs if you have more than one battery like the above FSB does. With that switch you can self jump-start or run off of either battery. In my FSB the rear battery is the "house" battery and most of the electrical that I have added to the vehicle runs off of it.
This is the front battery in the same FSB with the battery switch shown, but more important to a two battery system is the black box with the yellow piece seen under the switch. That is the Blue Sea Systems Automatic Charge Relay that charges both batteries regardless of the switch setting (unless that is 'Off').
A point of concern if you're going to build a box under the rear seat, do not make the box from aluminum. Make it from steel and weld it into place. Bolting an aluminum box to the steel structure will be the cause of the corrosion that I'm guessing that you're hoping to avoid by using aluminum. All it will take will be a little moisture to get between the the two metals and instantly you've got galvanic corrosion going on.