In that case, the recommended method is to use a filling funnel which screws into the top of the ABS unit to allow a head of clean brake fluid to feed the pump whilst bleeding and prevent air getting in. Some say you can do without it, I say use one. If it wasn't needed BWM wouldn't bother with one.
The brake system has four circuits. Two from the handlebar lever/foot brake to the ABS pump act as pilot operating circuits. The other two go from the ABS pump to the front or rear brake calipers respectively and are the operating circuits.
You bleed the ABS pump and the calipers, refilling both the handlebar reservoirs and the ABS pump internal reservoirs. I can't remember the exact sequence for bleeding so you'd be best to do a search for the info or get hold of a RepROM DVD.