Apparatus and method support the configuration and testing of therapy parameters for a medical device system in the treatment of nervous system disorders. With the embodiment, the medical device system operates in a manual treatment therapy mode, in which the medical device system evaluates a set of information that is indicative of a system configuration. The medical device system determines if the set of information is acceptable. During the manual treatment therapy mode, the medical device system applies therapeutic treatment to a patient in accordance with the set of information. If the patient cannot tolerate the therapeutic treatment, the user indicates so through a user interface. The medical device system may associate the patient's intolerance to therapeutic treatments that equal or exceed the patient's level of tolerance. Moreover, the medical device system may use this information to prevent a delivery of therapeutic treatment that exceeds the patient's level of tolerance during a run mode.