The application configuration is stored in the PIC microcontroller's internal EEPROM in the first 256 bytes of data. The structure of the data is defined in the APP_CONFIG_ENUM enumeration.
The device's default configuration is set in the eeconfigArray array in the appcfg.c file. This array will define the values for the entire APP_CONFIG_ENUM, which contains all application configuration. At compilation this data is added to the hex file, which is then written to the PIC's internal EEPROM at programming. Some programmers will have the options during programming not to program the PIC's internal EEPROM memory. It is important to enable the programming of the internal EEPROM to have this default device configuration written to the EEPROM.