I take it your using a automotive subwoofer amplifier? If so there are wire size requirements and they pull a lot of power. Most wires that run to the stereo are to small to supply much current. Another thing to consider is if you are depending on battery power alone a large amplifier will run a battery down very quickly if not plugged into a charging source.
Unless it is a very low power amplifier it will require a dedicated wire to the battery and ground. My amplifier requires a 4 gage wire and its own 30 amp fuse.
Keep in mind the ground wire will need to be the same size as the power wire as well.