First off, You gotta have a hi output alt. If ya' don't try 4alterstart.com. I had a buddy once that wired his in the trunk. You have to run power to the batt(s) from the alt- and if u do decide to wire it for the trunk, make damn sure u have a sufficient GROUND. Also you need some sort of battery box-cheap rednck way: use a couple of 2x4's(underneath). You must secure them/it, tho'. Run 1 battery(cranking) by ITSELF. Run the other somewhere else(trunk mebbe)....U want all ur system equip to run off the one in the trunk. Coo'?
you'll need a battery isolator, which connects to the starter battery and runs to the dedicated acessory battery in the back of the car. if you use more than one battery for the audio system, wire them in parallel connecting the Isolator output to the first of the bank of batteries. you'll want to consider a high output alternator as mentioned above to handle the increased recharging demands of the additional batteries as well.