If your controller is paired then you might be able to configure it “the regular way”:
– Make sure you’ve got a keyboard or controller connected that Retropie “has recognized”
– Press: “Start” (or Enter on the keyboard if that’s configured to work as a controller)
– Go to: “Configure input > press “A” on the controller (or X on a keyboard)”.
– Follow instructions on screen, i.e. hold a button on the BT controller to configure it.
– If RetroPie does nothing after pressing a button on your controller then it might not be not be registered as a controller or input device via bluetooth.