My S4 had the same setup...3 tether hooks, and 4 LATCH connectors.
Don't remember if it was in the manual or not, but you were not supposed to use the LATCH connectors to secure the car seat in the middle as it was unsafe for some reason.
The E90 may be the same.... a quick call to BMW USA might give you the answer?
More info here (second "6Q" question):
http://www.car-safety.org/latchfaq.html