Grounding the mobo and case got rid of my alternator whine. Just attach a wire to one of the mounting screws for the mobo. Also attach one to the case maybe on one of the screws holding the cover on. Ground to a common place on your car frame, preferrably the same as your PSU and other things.
The onboard sound from the Epia is notably poor. I got an Audigy 2 and am very happy with it.