You have two ways to pair the controller. You need a keyboard or mouse for both though.
1). From the ouya launcher go to manage > pair controller.
Once on this screen, hold down the OUYA system button on the controller until the two center LEDs start flashing, then let go of the button. The controller is now in pairing mode and the two center LEDs will flash until the controller is paired. May take up to 30 seconds.
2). in xbmc go to programs then Android Apps/programs. Then select either settings or advanced settings. I'm not near my box so I'm going by memory.
From here go to Bluetooth which should be the second option down. Click search for devices in the top corner and put the controller into pairing mode as above. The two should connect.