Just use the standard guidelines for fusing wiring: the fuse (or in this case circuit breaker) is immediately after the source. And every power wire must be fused. With what you have, I would look at the four batteries in the trunk as a "battery block" and deal with them as if they were a single battery. So instead of a single battery you have four individual batteries connected in parallel, and the wiring connecting one to the other is protected by a circuit breaker close to the source, which is the battery on the upstream side. The breaker will trip, or a fuse will blow, whether the excess current comes from the source side or the downstream side.
This block of batteries would fall in line after the isolator and before the caps (which you might also look at as a "capacitor block". You can buy connectors for multiple caps that allow for fusing of the power wire between them, or just put in a fuse or breaker at that point, too, as well as after the second cap. After the caps would come a fused distibution block, from which you will send (fused) wires to the amplifiers. You will have to purchase the proper distro block and any additional fuses, fuse holders or circuit breakers that are needed.
Isolator > wire w/ breaker near source (isolator) > 1st battery pos term > wire w/ breaker near source (1st bat in trunk) > 2nd batt pos > wire w/ breaker near source > 3rd batt pos > wire w/ breaker near source > 4th batt pos > wire w/ breaker near source > cap 1 > wire w/ fuse near source > cap 2 > wire w/ fuse near source > fused distro block > amps.
The fusing in the distro block will protect the wiring to the amps, and the amps themselves will be protected with their own fuses. The "source" is the power supply from which a wire goes to another component and there is a new "source" with the addition of each component in the chain which begins at the alternator. Fusing is done near the source, and either breakers or fuses can be used to protect the wiring between power components. Grounding of the caps and each battery, as well as the amps, is to chassis. You can use a grounding (unfused) distro block to help make it more manageable.
And just as with the use of multiple batteries in any appliance, the 4 batteries in the trunk should be of identical age and use. But unlike the batteries in a flashlight, where series connecting adds the individual voltages together to form a sum...your batteries are connected in parallel (pos to pos) so that 12 volts will be maintained and amperage capacity will be summed.
Build the box so that it performs well in the worst case scenario and, in return, it will reward you at all times.
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