Vehicles equipped with a dual battery system have several different modes, depending on the status of the main systems battery. The most common mode links the two batteries together, taking the load off the main systems battery and charging both batteries. The dual battery system also has two shutdown stages as well as an emergency mode that completely switches all functions from the main battery to the auxiliary battery.
During a stage one shutdown, some of the vehicle's electronic components stop working. A stage one shutdown only disables a few of the vehicle's electronic features, such as the rear windshield defroster and heated seats. A stage two shutdown disables internal power outlets and lowers the climate control fan speed. During an emergency mode shutdown, the battery control system switches all functions to the emergency battery, and only essential electronic systems continue operating at full capacity.
The Auxiliary battery does not typically last as long as the Full size battery and we start to see failure on these as early as 2 years. So, if you are having issues with some of the convenience features on your car, it just may be that!