Yeah it's definately not the Sub doing it as long as the electrical system is in good working order. It's when youre charging system is dieing, that the sub will make it die much faster! Once you get it fixed, you'll be fine with the sub, you are probably only runing 2-300 watts, so you should be more than fine. To take into account, i run a 0 Gauges wire from my battery to amps, and it does not kill the amplifier (think how many amps that draws).

Also, when you hook up a new alternator, run a 4 gauge wire with a built in fuse straight to the battery, and upgrade the ground wires between the frame, body, engine block and battery, you will get some extra amps from your battery and it wont work your alternator as hard.