EEPROM Microcontroller
The way I usually do it is to have an "EEPROM Is Valid" flag in the EEPROM.  Then the main program contains a set of defaults, and if the EEPROM isn't "valid" it loads the defaults into the EEPROM and sets the valid flag.

That way the first time the board is powered up it sets up the EEPROM for you, but subsequent powerups just use the EEPROM data that's already set.

Also has the benefit that it can be reset to factory settings if you want.

Of course, it's then up to the main program to update those values as needed, but without knowing what your system does I can't comment on that.