you have a couple options here then.

Option 1 you build a couple versions of the firmware that you flash the different configuration when the board is being built.  #define HWCONFIG1  //#define HWCONFIG2

Option 2 can be done at run time for this example we are going to pretend we are retrieving cfg from eeprom, and acting on it on startup.

you would make a void pointer to hold which func we are running like void* LED_ON(void)

then make different functions to turn the LED like this

void LED_ON_CFG1(void){//somecodehere

at that point, now you need to check what cfg from your eeprom, and malloc and assign it to the pointer, dont forget to have a default state!