You should be able to hook it up through the "line in" connection. Take it to an audio shop for advice. The "high end" factory stereos always cause more problems as they sometimes use weird ohm ratings that could damage your amp or your factory deck.
If you want really good sound quality you're best off taking out all of the stock equipment and starting over. The money spent on the Bose or Infinity sound systems from the factory is always a waste compared to what you could've gotten at your local audio shop.