Quite a different car but I suspect it will be similar in design. I have a Euro 1998 E36 M3.
It has (had) a cassette headunit with 4 channels of 8V (I think) "line" level unshielded outputs. They feed into a 10-channel amp in the boot somewhere with each channel driving individual speakers 3 per side in the front and 2 per side in the back. The crossovers are built into the amp.
Do you have a DSP option on anything? If so they tend to run digital all the way to the amp (or possibly DSP unit) in the back.
Apart from the DSP stuff (not available on E36s) I would guess that an E39 has a similar design.
I ran the empeg's line level outputs direct into the amp. It works but isn't quite loud enough due to the lower level output of the empeg. Generally I run -5 to 0dB output on the empeg when I'm by myself. At freeway speeds and the windows open, it's not really loud enough. Only just not loud enough though...
Antenna is likely to be powered. On mine, the amp remote line also drove the antenna amp line, so no extra work was needed (although the antenna connector was a little loose causing really bad static).
BMWs are notoriously difficult to get quiet installs. I have zero whine in player mode and faint whine in tuner mode - just enough to annoy.
An E39 will have IBus. It's a single wire semi-proprietary bus. It will like connect a lot of things together including stuff like the radio, instrument cluster, windows, sunroof, steering wheel controls etc. Generally the less important stuff. The protocol is pretty well known and with a bit of programming an IBus to empeg interface wouldn't be too hard. I had empeg faking a CD changer initially (later E36s used IBus only for the CD changer). See http://groups.yahoo.com/group/HackTheIBus/
Have a google around. I'm sure I've seen some E39 installs of regular car audio.