Methods using multiple timing channels for electrode adjustment during set up of an implanted stimulator device are disclosed. In one embodiment, at least two conditions of electrodes (i.e., electrode combinations, pulse widths, pulse frequencies, pulse amplitudes) can be “simultaneously” tested by providing each condition in its own timing channel. In a preferred embodiment, the pulses in each of the timing channels are interleaved and non-overlapping to preserve the ability of the patient to assess the therapeutic feel of both and to allow some time between pulses for recovery. As well as allowing two sets of electrode conditions to be gauged at the same time, the technique allows the electrode to be manipulated during set up with ease and with a reduced possibility of providing the patient with erroneous results. For example, the two conditions in the two timing channels can comprise initial and target final conditions, and transitioning between from one to the other during device set up is facilitated as compared to the prior art because concerns with electrodes having inconsistent properties in both conditions are alleviated.