Keep in mind that a 2nd battery will be an extra load on the electrical system when the car is running. They are usefull however if you like to listen to the stereo a lot without the car running. When the car is running the alternator supplies the juice to the car's systems, engine, and stereo, the battery only comes into play when the car is being started or there is a large draw on the electrical systme which causes the voltage to drop to the level of the battery or below, at which point the battery will then supply current to fill the demand. Once this peak draw is over the alternator must still power everything else while recharging the battery.
A capcitor works must like a battery it stores a set amount a electical energy that can be discharged very fast. Which means that it also is an extra load on the electrical system. The idea in using them is that periods in which the stereo is drawing a lot of power is very brief and the Cap can supply the extra current during the demand, and in between the peaks when the system is not demanding a lot of current the cap will draw power from the alternator and recharge itself before the next peak. It will hopefully act like a buffer just smoothing out the bumps in the voltage between high demand and low demand.
That being said I would personaly choose a high output alternator since the cost would be not too much more than that of a Cap and will provide all the juice the system will need. This all of course depends on the size of the system and how big the stock alternator is. Some cars have beefier electrical systems to begin with. Remember Caps and batterys don't make power they only store it, it would be more logical to just upgrade the source of the power first.
BTW you will be happy with the JL amp, I'm running a 300/4 to power the front speakers (5.25XR comps and a set of 6W0 woofs) and love this thing. It looks good is built like a tank and has an awesome crossover.
Oh, did I mention it sounds awesome too?
