As I didn't have a EEPROM on our custom board, is it possible to store the MAC Address in eMMC then read from eMMC when running Linux kernel.
If yes, how to configure it?
You could store MAC address in software or in U-boot environment configuration, which is stored in the same memory as u-boot.
Under u-boot prompt, you could configure MAC addresses as the following.
=> setenv eth1addr 00:04:9F:06:04:49
=> setenv eth2addr 00:04:9F:06:04:4A
=> setenv eth3addr 00:04:9F:06:04:4B
=> setenv eth4addr 00:04:9F:06:04:4C
=> setenv eth5addr 00:04:9F:06:04:4D
=> setenv eth6addr 00:04:9F:06:04:4E
=> setenv eth7addr 00:04:9F:06:04:4E
=>setenv ethaddr 00:04:9F:06:04:48
=> saveenv