One of my 5-night stays was master-billed by my company, resulting in a total due of $37.00 upon check-out. I only got rewards credit for what I personally paid, not for the hotel stay itself. I was told by a Marriott Rewards Program Supervisor that this is a policy common to all hotels in the industry.
When I stayed at a Courtyard and my company required being direct billed, I made the reservations under my name and still received the points. But the direct billing did result in my earning less points since I couldn't pay the bill with my Marriott credit card!