All input to the pump needs to be open @ 100%. So if you are pumping from the BK or MLT, if they are going to the input side of the pump, that valve should be open all the way. Having a valve on the output side of the pump is the best way for controlling flow. Reducing the flowrate on the input side can cause a loss of prime.
On a side note, its best to use the pump in a vertical fashion. Input at the 0600 position, and output at the 1200 position. This aids in reduction of air pockets and less chance of losing prime.
I went through a lot of headache with my pump before yeilding to others suggestions.