Audio Systems: car audio problem- loud thudding noise coming in over very low music, portable cd player, antenna wire

Question
okay so my bf set up my system.. I have 2 12's in a box in the trunk and a 1600 watt lanzar vibe amp.
 I have 2 back speakers whip audio with a rockford p. amp.
and also have 2 front speakers(logic, I know there bs)
that stand alone.

okay so this is the deal, we have set up everything before, always been fine, everything's always worked great, we went to hook up the new back speakers we bought so we could listen to our music finally..
and we put everything in the car... we were putting the head unit back into the dash and something happened to the remote wire and the antenna wire... and the speakers started to make a high distorted sound(Not the hissing sounds) at all.. a thudding sounds, and its repetitive.
I've been looking for 4 days already and can't find anything
god bless have a great weekend
cat"


Answer
First, test the subs/amp combo by feeding them a known good signal. I would use an ipod or portable CD player with a headphone to RCA cord. Plug it in, start the car, and see if the thumping continues. If it does, have the amp repaired.
Otherwise, the CD player in the dash may have been damaged by the wires being shorted out during the install like you described.