2000 Dodge Stratus: CD won’t install

I know nothing about cars, but my boyfriend is trying to install a new cd player in my 2000 Dodge Stratus.  He installed the same exact stereo in his van (also a Dodge) and it worked fine.  At the moment, my Stratus has a factory am/fm tape deck.  He tried using a generic wiring harness with the first cd player.  When he hooked all the wires up the cd player works fine, but you only get sound out of the small speakers (tweeters?) on the dash not the ones in the doors.  He tried again and went to Auto Zone and bought the wiring harness for my car, but it still has the same problem.  There's a brown 'mute' wire that he's never seen before, and no one seems to know what the problem is.  I looked at the vehicle wiring diagram for my car on this site and it isn't listed there either.  I've seen several posts on forums that talk about bypassing the factory amp and installing a new one.  I'm not really interested in a better amp or speaker system, I'd just like to be able to play cds.  Does anyone have any thoughts on this?  I'd really appreciate it; we're about ready to pull our hair out. :) Thanks