Methods and systems are provided to control a configuration of a neural stimulation (NS) system having an NS device coupled to an NS lead. The methods and systems change between configurations of the NS system and collect cardiac signals from a patient that are representative of cardiac rhythms experienced by the patient over a period of time and in connection with multiple NS configurations. The methods and systems derive, from the cardiac signals, characteristic values for at least one physiologic characteristic indicative of at least one of normal and abnormal cardiac rhythms in connection with the multiple NS configurations; and select, from the multiple NS configurations, an NS operating configuration to be used by the NS system based on the characteristic values.