From the Windup How a Pitcher Can Legally Step off the Rubber
With runners on base, a pitcher must step backward off the rubber with his pivot foot (RHP – right foot) and then drop his hands to his side. If the pitcher steps backward with his stride foot, it is the beginning of his normal pitching delivery so if he stops, it is a balk.
When stepping off the rubber, the pitcher must do so without hesitation or interruption and must make no movement normally associated with his motion to pitch.
From the windup position, the pitcher may step directly and throw to an occupied base. For instance, with a runner on 3B the pitcher, without disengaging from the rubber may step and throw to 3B. He may also turn and fake a throw to 2B.
Sometimes a pitcher will balk when there is a runner at 3B and the pitcher is on the rubber in the windup position and then changes his mind to pitch from the stretch and he fails to step off before shuffling his feet to get in the stretch position.