Your car's GPS antenna does feed into the "Trimble" module that was separate with the MKII. You need to disconnect the antenna cable and move it over to the little coax antenna plug on the MKIII. I believe that the Trimble module is located almost on top of the nav computer.

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2000 E38 750iL Highline Edition, Upgraded with the lastest 2006 X5 Electronics
MKIV Navigation, 16:9 Display, Bluetooth, TV/Video with Backup Camera, Sirius, and Aux Input