not having looked at my stereo I am not certain but I do know that there is an amp. I do not know if there are mulitple amps one for the highs and mids and then a second for the bass. In any case it sounds like you lost your mids and highs, you could have burned out your amp.
Again I haven't looked to know the set-up but it might be a place to start. When I have a problem and don't know where to start I will call the dealer and explain the problem(making it sound as if I am going to bring in my car). Many times they will tell me where to start looking and that is enough for me to figure out the rest.
There are a ton of guys here who really know their stuff, I am sure someone will give you better advice than that.
Good Luck
Peter