If the brake fluid res. empties, will it foul up the ABS system? Or can I just refill it and bleed the system without any problems?

 

Although I am not a specialist on this, and I would suggest you take my advice with a pinch of salt, I would say that you shouldn't have any problems with the ABS bleeding the system.
However, why did the brake fluid empty in the first place ? Maybe you should be addressing this issue first !