This depends on your tastes, but the EQ stays the same regardless of input, which can be an issue because each input is so different. Satellite radio is so compressed and mid-rangey, it sounds very different from a CD or iPod, etc. My old Tundra let you set the EQ for each input, which I liked a lot.
The "best", clearest sound I get out of mine is sending a pre-equalized signal from either my iPod or iPhone, usually the "Rock" or "Treble Booster" setting, and then setting the EQ from there. I boost the treble again, cut the mids and slightly cut or leave the bass alone, depending on style of music. Play around and see what works for you.
