Currently, you can only run two eMAC ports. They must be either ab or cd. Each pair has its own FPGA bitstream. Not all systems have all ports functional. To find out which ports are functional, telnet to the BMC and look at the signon message. For example, the following line indicates that only port B is functional.
Usable GB ETH 0100
When you have two enabled eMAC ports, how are the divided among the cores? The first port takes the first 24 cores, and the second port takes the next 24 cores. This is true no matter how many cores you boot. If you just boot 24 cores, then your second eMAC port is not used.
As another example, consider the following line from the signon message.
Usable GB ETH 1110
Here ports A,B, and C are functional. If you load the ab bitstream and configure both eMAC A and eMAC B and boot 48 cores, the first 24 are on eMAC A and the next 24 are on eMAC B. If you boot 36 cores, the first 24 are on eMAC A and the next 12 cores are on eMAC B.