By default, the gamepad is in pilot mode. In pilot mode, the left stick controls the ship’s facing, and A and B accelerate and decelerate. Holding down the left stick engages warp; clicking it again disengages. Primary and secondary weapons are linked to the right trigger, and special weapons to the left.
Holding down the right bumper puts the ship in select mode. In select mode, pressing A, B, or X while pointing the left stick will select objects. Y will order your control object to go to your target object. Clicking the left stick will transfer you to your control object.
Holding down the left bumper puts the ship in target mode. In target mode, pressing A, B, or X while pointing the left stick will target objects. Y will engage autopilot. Clicking the left stick will set your own ship as your target object.