First thing I would do is unplug one of the sub wires and switch the polarity. Maybe they removed the box for some reason and when they hooked it back up they switched polarity and put the subs out of phase. That is the easiest thing to try and the most common screw up.
Them Pioneer 6300's have a wide array of controls for the pre-outs. I am thinking they disconnected the battery resetting the radio's settings. That's the only thing I can think of that could have happened when putting in an alarm.
How knowledgeable are you with the use of all the functions on the deck??
Sorry I wasn't more help... real difficult to tell you what the problem is without hearing the problem.
San Antonio, Texas
Ive been trying everyting and adjusting the gain has helped somewhat but the bass still sounds horrible. Thanks to everyone that tried to help me, but if i want this problem fixed i think im going to have to cave in and go pay for someone to diagnose and fix the problem. Once again thanks to all that tried to help.