Well, for one, if your going for Audio Quality your EQ should be flat. I don't think your problem is media engine. I think it's a combination of the quality of MP3 and soundcard. How are you piping your audio from the PC into the stereo? Standard RCA? How heavily are they insulated.
I myself run straight TOS-LINK to my Alpine DSP. Zero sound quality loss. In fact, in 5.1 applications such as DVD playback my car sounds better than my Pioneer Elite setup at home.