In one embodiment, a method for the controlling of the stimulation pulses being delivered via electrodes to a patient during the programming of a pulse generator using a controller device and selecting of a minimum amplitude that corresponds to the minimum amplitude for which the patient can detect stimulation selecting an electrode combination defined in the controller device setting the stimulation amplitude making a determination of the amplitude for the stimulation pulses is greater than the perception amplitude, and if so, changing the amplitude of the stimulation pulses to be less than or equal to the perception amplitude and if not or subsequent to the changing of the amplitude, changing the selected one of a plurality of electrode combinations to a different combination.
