The present invention relates to a neuromodulation system comprising an external control device for programming an implantable neuromodulator coupled to an electrode array implanted within a patient, the external control device comprising:a user interface;telemetry circuitry configured for communicating with the neuromodulator; andcontroller/processor circuitry configured for, in response to input into the user interface, directing the neuromodulator via the telemetry circuitry to deliver super-threshold electrical modulation energy in accordance with a super-threshold modulation parameter set, and sub-threshold electrical modulation energy in accordance with a sub-threshold modulation parameter set, wherein the super-threshold modulation parameter set and the sub-threshold modulation parameter set are contained in a hybrid modulation program.