Capacitor & Dead New Battery

Hello, I have a project car I am working on. It is an 01' SS Camaro and it is having body work done on it slowly on weekends when time can be found.  I already pretty much installed my sound system.

I have 1 audiobahn (1000 watt RMS- can't remember model number) and a smaller audiobahn amp for midrange speakers.

I upgraded alternator  to a high output one ( can't remember the amps for that off the top of my head either) and I also bought the optima yellow top battery.

Now the car has set up for about 4 months with no work done (or cranking either) as I got extremely busy with work and exams and the car is kept at my parents home while I am at school during the week.

Capacitor is digital and seemed to stay on all the time and the battery was DEAD. I don't know much about capacitors, but is this normal? During normal driving conditions, would not cranking the car for about 3 days kill the battery? Should I install a switch to turn the capacitor on when I am driving. It is wired from battery to capacitor and then splits to each amp.

Just need a little advice. Thanks