Since you have the standard amp, the swap is a little easier. You could simply swap the radio module by removing the BMW radio and then connecting the aftermarket radio to the BMW's radio plug with a simple adapter. That would give you new features, but it would not improve the sound that much, because it would still be playing through the stock BMW amp.

If you replace the head unit, you could also choose to replace the amp in the trunk. This would give you more volume and cleaner quality sound. That would take some wire splicing to tap into the audio signals from the radio and then feed the amp's signals into the speaker runs. Plus, you would need to install some "passive crossovers" for the speakers, because the BMW amp has internal "active crossovers" that you would need to substitute. This and an aftermarket head unit would improve things a great deal, but you would also need new speakers to capitalize on the amp improvements...

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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