Mids and Treble at 0/neutral. I think I've set Bass to +3; but there is no ideal setting, this is too little for some songs, yet too much for others. And I'm too lazy to fiddle with the radio menus to adjust it all the time. Generally I'm very happy with the sound.
I don't know about breaking in the speakers, I've got my car when it was about 6 months old.