The bottom line is that if your alt isn't big enough to satisfy the regular demands put on it, no ammount of batteries, caps or a combination of the the two will keep it from dying and will actually cause it to die quicker. Batteries are only of real use when the system is run with the car off. Caps have a place, but are rarely used in the correct situation. The only time a cap might be of use is to eliminate the quick voltage drop caused during a musical transient when an alternator that is big enough for the system is upping its current output (the change from 50A output to 100A output is not instantaneous). This will reduce the dimming of lights in a system that has an adequate alt.
Batteries have tons more capacity than a cap, yes, but they only supply that current at their discharge voltage which is usually in the neighborhood of 12V. Since it is the transition from the alts working voltage (usually over 14V) and the battery's discharge voltage that causes the dimming of the headlights, a battery doesn't do you any good. The cap begins to contribute current as soon as the voltage drops below the normal operating voltage of the alt. Since you only want the current for the fraction of a second it takes for the alt to catch up, total capacity is not that big of a deal, but the bigger the cap the smaller the drop in voltage in the mean time.
This is also only a consideration on a daily driver system. If you are looking for an SPL comp type system, the cap is a drain on the electrical system after the first fraction of a second. This is the main reason that you see SPL vehicles with tons of batteries. The batteries are the primary source of current for the system.
