The present invention teaches methods and apparatus for user control and operation of physiological modulation, including neural and gastrointestinal modulation, for the purposes of treating several disorders, including obesity. This includes programming of neuromodulatory signal for the modulation of autonomic neural and neuromuscular modulators, used to modulate tissues, including the afferent neurons of the sympathetic nervous system to induce satiety and efferent neurons to modulate metabolism.