A system, method, and implantable pulse generator (IPG) device that stores, on the implantable device, two or more treatment-protocol stimulus programs, each preferably having one or more stimsets, preferably as prescribed by a physician. The IPG communicates with an external patient programmer (EPP) to determine which of the stimulus programs should be run at any given time. Programs stored on the IPG are uploaded to the external device, and a selected program retransmitted (either the program itself, or selection information identifying the selected one of the IPG-stored programs) to the IPG for execution. An advanced programmer is used to read and write program instructions to the IPG. In this way, the patient is capable of carrying two or more program options with him, and if the patient uses an EPIPG, he can use any available EPP to power and operate the EPIPG.