Starting up a freshly built BBB

I have a developer working on integrating the BBB design with a cape into a single PCB. When the board is assembled, I assume that at a minimum, we need to program the onboard EEPROM with parameters to tell the system what it’s booting up with. Is this done through the JTAG port? Do any of other parts need to be flashed before it will recognize and boot from uSD?