Only thiing dual batteries is gonna do for you is buy more time before they die. Any more amperage draw than the alternator can supply is taken from batteries. The cap in the rear in NO way provides more available power, it simply supplies its stored energy much faster than any battery ever will ( capacitors discharge in microseconds) during those bass spikes in the music. If you hear a high volume system that sounds muddy and the speakers aren't bottoming out like alot of peeps drive them to, its cause the electrical system couldnt supply enough amperage fast enough for that musical peak.
Only way I see you running reliably is to have a custom alternator wound and mounted as a secondary unit , leaving the stock alternator to drive everything else in the car. Also, if you do this, run the head unit off the same alternator and battery as the amps, not the car's electrical. If you do all you are doing is causing a ground loop between 2 seperate electical systems, and this can lead to alot of unpleasant side effects.