I am able to get it working now on Emulation Station but on reboot it needs to be manually discovered again, I wrote the script that finds the MAC address and make sure it found but it does not seem to be working.
#!/bin/bash
sudo bluetoothctl << EOF
power on
connect [MAC Address]
exit
EOF
I made the correction and was given a prompt for a pin I set it to 0000
It seems to be working fine now
#!/bin/bash
sudo bluetoothctl << EOF
power on
connect [MAC Address]
connect [MAC Address]
exit
EOF
Would that be the only change to make two of the same controllers be found on boot?