there are two basic methods for aligning motor with pump,gearbox, etc., one is rim & face method in which one dial indicator pointer positioned on the radial side and the second on the face of the movable machine (motor) coupling to calculate the misalignment. the second method is reverse indicator method in which two dial indicators used to measure only the radial deflections in both (motor and pump) couplings for misalignment calculation.
the reverse indicator method is the precision method of alignment than the former one.
if you search for reverse indicator method in google you will find the entire details.