You have two questions, first when the standby rudder PCU is activated automatically by the FFM is hyd A or B shut off to the main PCU? Answer No, when the FFM detects a pressure diff on the main rudder PCU it simply activates the standby rudder PCU and illuminates the STBY RUD ON light.
Second, how would it know which system is faulty during a force fight? Answer, it doesn’t need to because both hydraulics remain on at the main rudder PCU.
There is no facility to switch off hydraulics just at the main rudder PCU. If you switch the flight controls switch to either OFF or STBY RUD it will switch off hydraulics to the ailerons and elevator as well as the main rudder PCU. The only difference between these two positions is that at STBY RUD you will also have standby hydraulic power to the standby rudder PCU.
I guess what you are asking is what if there is a rudder hardover, will hydraulic power be removed from the main PCU if this is the source of the hardover? Answer, NO unless you switch the flight controls switch to either OFF or STBY RUD. This is the last step in the Uncommanded Rudder/Yaw or Roll procedure. It is only necessary to do this on the B system because you have an RPR reducing the pressure on the A side. In fact on the NG you also have two load limiters reducing pressure on both A and B sides so the potential problem is reduced further.
BTW I wrote a 13 page article on this subject here
and it still confuses me!