Mark this one as solved. Here is the current procedure for getting these to work:
Update 8bitdo firmware. Clear all previous paired Bluetooth devices. Make sure 8bitdo hack is OFF. With only a keyboard plugged in and both controllers off, turn on and pair each controller. Take one of the paired 8bitdo controllers and once back in emulationstation, hit start and assign the buttons.
Very important, you MUST assign the buttons in ES even if you have previously assigned the buttons while the controller was plugged in. The controller on Bluetooth is actually viewed as a different controller than when it is plugged in so your button map doesn't transfer over. Enjoy!