Easy. All you ever need to root for is for USF to beat UCF; none of the other schedule minutae matters.
Having said that, I personally I want them to go winless. While I know a good rivalry with strong teams gets good ticket sales, tv ratings, rankings etc, it doesn't do me any good. I have to deal with hearing their alums frequently enough. If you want a rivalry, find a school that doesn't encourage their fans to delude themselves into believing they are national champs.
Final answer: Better for me if FAU upsets, better for USF football if UCF takes care of biz and USF beats them in turn