Just bought a new factory head unit to go in my 99 e46 so I could add a CD changer or ipod. (Old one did not have a "Mode" button) I went to install it and there is no place to plug in the antenna. What am I missing?

You need to get an adaptor. newer units have a different antenna

Here's the adapter you need:

BMW Business CD Radio Antenna Adapter
http://www.europeanautosource.com/product_info.php?products_id=292

Get this and you'll be set up in no time.

Thank you very much.

One more question. It looks like I have 2 antenna wires in the car (I'm sure that's not the case, but that is what it looks like). One with the old larger jack, and one that looks like the smaller new style. The old business CD has a spot to plug both in. The new business CD only has the smaller input. If I get that adapter that converts the larger jack to go into the smaller input, then where does the wire from the car with the small jack go? Do I not need it anymore? What the heck is that wire anyway?

We're converting to a single diversity antenna, the other cable is not used.