How can I program my custom board EEPROM??

Hi, I am a new one at this area. My partner and I made a copy of beaglebone black on our board. We just deleted Ethernet and HDMI. We still used 4GB DDR3, 4GB eMMC and a empty EEPROM. We will boot it from uSD just like the beaglebone black. The image file is BBB-eMMC-flasher-debian-7.8-lxde-4gb-armhf-2015-03-01-4gb.img.xz ". Because the EEPROM is blank so it would not boot. Learned there is some pinmuxing that takes place from the information in the EEPROM that was necessary.

The question is how will we do about the EEPROM to boot our board properly? Can we just copy the files from EEPROM of original Beaglebone black to our custom board EEPROM?

Best regards,