The conferences will send a list of their crew(s) to Steve Shaw, the National Coordinator and his staff. I don't know if Shaw alone will assign the playoffs or he'll do it via committee, but however the assignments are done, the conferences' crews will be sent to a game not involving a team from their conference.
It appears from last year that each of the "power" conferences sent 2 crews to the playoffs. From what I can tell, 4 crews -- 1 from each of the SEC/B10/ACC/B12 -- worked 2 games. The other crews worked one. Who knows if they'll change that system, but I think part of it is they don't want a crew working that hasn't worked a game in more than a month. So if they added a third SEC crew, for example, that crew might have gone from late November to late December without having a game.