Adding caps under the hood will do nothing, besides burn up your cash. As long as your power cable to the trunk is of acceptable gauge, your voltage drop will be within acceptable tolerances. If your cable is too small, having a cap will do nothing for the unacceptably high voltage drop. It will still drop the same amount by the time it gets to the trunk. In fact, it may be ever so slightly worse, owing to the fact that you have even more connections in your power cable. The purpose for the cap is twofold.
1) To provide CURRENT when the amplifier demands it, thus minimizing voltage drop, BUT the cap must be installed within 18 inches of the amplifier. Voltage drop will change, based on the current and distance. Example: If you have a 4 gauge cable, and your acceptable voltage drop is, let's say .5 volt, and you are only using it to carry 10 amps of current, you can go 10 TIMES FURTHER with that same #4 than if you were using a #4 for 100 amps of current. What this means is, if you put the caps under the hood, and if your amplifiers are pulling 100 amps, and you are using a #4 wire to your trunk, you will have EXACTLY the same voltage drop at the trunk as you would WITHOUT the caps under the hood. Now, if the cap is in the trunk, and your amplifier requires a 100 amp gulp of current, the voltage drop WILL still be present, but with the cap NEXT TO the amplifier, the voltage drop will be filled in by the LOW IMPEDANCE OUTPUT of the capacitor, thereby filling in the voltage sag generated by the voltage drop over the power cable.
and 2) filtering, which is a single word describing the above process, so really, a cap only does one thing...
The second battery is, indeed, the better way to go. If you go this way, you DO NOT NEED ANY ISOLATION! You have a HO alternator, you will have PLENTY of current to charge both batteries, and keep them charged. For those that believe an isolator is necessary, I will tell them right now that is wrong. A relay type of isolator will always favor the lowest charge... which one is that? Most likey the system battery in the trunk, and thus, this battery will demand more charge time than the battery in the front. This will mean the front battery is almost always undercharged, mandating replacement sooner. The solid state type (diode isolation) will allow too much voltage drop, and unless you have an EXTERNAL voltage regulator for the alternator (and almost all of them are internal today) and/or a voltage monitor/control regulator to maintain proper voltage to BOTH batteries, they will both be in a largely undercharged state, again mandating replacement sooner than necessary. It is IMPERATIVE, therefor, that your batteries be the same type, manufacturer, CCA, reserve time, and age. If they are significantly different from one another, you WILL get parasitic current drains, either one way or the other. (front to rear, or rear to front) This will cause one battery to die faster than the other. If you START with identical batteries, you will, from that day on, be able to (and, unfortunately, be required to) simply buy two batteries at a time, and replace them simultaneously... I agree, additional expense, but what are you going to do? - ah, the necessary evils of our craft and love, hmmm?
Yes, a second battery will give more reserve time, but it will also provide better current and voltage stability than even a cap could. A cap is ALWAYS optional, but with a second battery, it becomes even moreso, and more than likely, completely unnecessary. With a second battery, your voltage drop will halve itself, because the front battery will be supplying half of the current demanded, instead of all of it, and the back battery will be providing half. With half of the demand being supplied by each battery, the charge on both batteries will drop equally, and the alternator will be able to maintain the charge to both correctly.
It all reminds me of something that Molière once said to Guy de Maupassant at a café in Vienna: "That's nice. You should write it down."