did you start having battery problem right after the install of the system? do you have a capacitor, if you do it might be sucking current from the battery causing a dead battery. i know this first had it happened to my frinds car with his cap and when i got it from him the issue migrated to my Tiburon and i was like WTF i had a tech at the dealer i was working at check it out and when i disconnected the cap the multimeter went way down for current draw from the battery, from like 2 amps to .00something from what i remember but that was 3 years ago.
if you have a multimeter disconnect the ground on your truck and run the meter from the neg terminal to the cable and have it set under amps to see the draw on the battery. then disconnect the cap and see if it goes down significantly, if it does thats most likely your problem otherwise the battery just might be junk and go to to dealer and see if they will give you a new one. if you do go to the dealer i would recommend you take out the subs and hide the power wire running to the cab just so they don't give you any hassle, some dealers will probably turn you down for running a system but some might not, guess its a hit or miss kinda thing.