In Emulation Station drill into Retro Pie Options, 2 Menu Items down click bluetooth.
1. ssh to plus1.
2. sudo ~/RetroPie-Setup/retropie_setup.sh
3. C - Configuration Tools.
4. Bluetooth - Configure BlueTooth Devices.
5. Make sure 8bitdo mapping hack (OFF - new firmware).
6. On controller Press Start to turn on controller.
7. Press and hold Pair Button on top of controller (next to orange led light) for 3 seconds to enter pairing mode.
8. LEDS on bottom will move from right to left (Faster than when trying to just connect normally)
9. Register and Connect to Bluetooth Device.
10. Choose bluetooth device you would like to connect to.
11 Connect to Pro Controller
12 Single green light on bottom is solid to indicate connected.
Also did Setup udev rule for joypad to ensure it reconnects on reboot