Should read this write up I did. Will open your eyes. Post number one
The ipod digital to analog converter is poor compared to good ones, your best bet is to use the bottom conector for a Low level output instead of the amplified signal coming out from the headphone jack. I use itunes as well but I import my music uncompressed from cd's than I use the bottom port on the ipod for full control voer it and better quality music through my head unit.
Car Audio 101