1. An integrated controller for an HVAC system, comprising: an interface coupled to an auxiliary controller of said HVAC system and configured to communicate therewith, said auxiliary controller having an auxiliary non-volatile memory; a processor, coupled to said interface and configured to direct the operation of said HVAC system; and a main non-volatile memory coupled to said processor and configured to receive a copy of main controller application information associated with said main system controller via said interface and store said main controller application information, said processor further configured to automatically send a copy of said main controller application information during manufacturing of said HVAC system to said auxiliary controller of said HVAC system to store as back-up data on said auxiliary non-volatile memory of said auxiliary controller.