currently you are relying on your chassis as your negative wire. in small systems this is fine, because V=I*R, and when I (the current being drawn for amp) is small, then V (the voltage drop between the negative terminal on your amp and the negative terminal on your battery) is also small. here R represents the resistance of your chassis. now in any car audio system the above V should be minimized, because this voltage is representative of wasted power (essentially going to heating up your chassis).
now in large car audio system "I" from above is also large, making "V" larger. to remedy this issue people make "R" smaller by instead of using the chassis as there negative wire, simply running a 0 gauge wire. furthermore, beyond the above considerations it is also desirable to have the same resistance in the negative and positive connections to the amplifier. that is why people will have the same number of positive and negative runs of wire. in competition it is not uncommon to see 8 runs of positive, and 8 runs of negative 0 gauge wires running from front to back- the high number of runs is to lower the effective "R" as much as possible.
so in your case this is how i would wire the system: 2 runs of 0 gauge from front to back, one is + and one is -. then have small gauge (like 12 or 10) + and - running from back batteries up to headunit. this helps prevent any ground loop issues and also makes it unnecessary to connect the rear batteries to the chassis. under the hood your good with the big 3. but now since your wiring your car audio electrical on top of your cars eleectrical, instead of integrating it with the chassis, one of the big 3 connections isn't as important- the one going from the negative battery terminal to the chassis. in the systems i've done i've just upgraded the + and - from the alt to the battery.