A method and system for programming settings of a medical device surgically implanted within a body of a patient. The system comprises a physician programmer, a patient programmer, an external neural stimulator, and a telemetry component being in communication with the implanted medical device, the external neural stimulator, and the physician programmer. The implantable medical device may be programmed using a two-phase process, a screening phase and an implant phase. During the screening phase, the physician and patient programmers may be used to roughly test the parameters of the stimulation to determine that the treatment therapy is efficacious. During the implant phase, the same physician and patient programmers may be used to fine tune the parameters of the stimulation.