A controller associated with a propulsion device in a marine propulsion system is configured to send and receive controller area network (CAN) messages on a CAN bus and has computer-executable instructions stored thereon executed by a processor of the controller to perform a method. The method includes receiving a configuration instruction CAN message containing a new configuration value, determining that the configuration instruction CAN message is directed to itself, and then receiving a reboot CAN message. Upon determining that the reboot CAN messages directed to itself, the controller writes the new configuration value to memory and then controls a power relay to power off the controller, ignoring a key switch value associated with the propulsion device being on. The controller then responds to the key switch value to power the controller back on, and then loads the new configuration value into the working memory of the controller.