1. A method for operating an implantable neural stimulator, wherein the implantable neural stimulator includes a programmable pulse generator circuit housed within a sealed case, an electrode array connected to the neural stimulator, the electrode array having a plurality of electrode contacts, and wherein various combinations of the electrode contacts comprise sets of electrodes through which an electrical stimulus may be applied, wherein the method comprises: (a) measuring and recording at least one perception point for at least a selected subset of the sets of electrodes; (b) estimating and recording perception points for unmeasured sets of electrodes; and (c) mapping the recorded measured and estimated values to magnitude levels for use with other designated stimulation parameters in a set of stimulus parameters that are programmed into said implantable neural stimulator.