Troubleshooting help

[dirtboy850]

I recently installed a new box and amp in a ford explorer. Everything was perfect and sounded great. Yesterday i went to install an RCA type bass knob and hook up the door speakers to a different 4 channel amp. Got everything hooked back up and the subs seemed very weak and produced a very ugly sound. Door speaks sounded great. I unhooked the bass knob and hooked up the rca's back to the way i had them. Subs still sounded very weak and ugly. I tested the subs on the 4 channel amplifier and it got a little louder and a little clearer( possibly because its not as big as the 2 channel amp). Not anywhere near how it used to be. I tried a new set of RCA's and still no luck. The HU has 6 preamp outs and i have them hooked to the sub out terminals. Need a little assistance on how i can go about troubleshooting this problem.