A quick call to service will give you the best answer. I have the factory aux and DICE iPod adapter installed. I can use either one. The aftermarket iPod adapters use the cd changer input. I think that you can have both the BMW iPod interface AND the aux input, but check with the dealer to be sure.
'07 530 Xi ,Auto, Gray, Black Leather, Premium, Cold Weather, Nav,Xenons,iPod,Sirius
'04 X3 2.5i gone
'07 X3 3.0si gone