I just had an alpine 7894 put in my 96 civic. Soundtrack did it, and i have already had problems with them so i don't recomend them. Now, i think they may have plugged my sub outputs into the rear outputs. In order to make my subs hit at all, i have to crank up the bass for the normal speakers. I don't think this should affect my subs, but its the only way to get them to hit, did they hook them up wrong or do your sub change when u adjust the bass?

 

slide the Alpine out of the dash and check your output connections.........it sounds to me that your sub out is plugged into the rear output of the radio. I have the 7893 so I am pretty familiar with your radio.