What I did was make 2 saves at the point where you have to choose your ending. It is right at the end as both finales contain 3 missions each. You know your at the right point becasue a dagger and $ sign appear on the map, so before you choose which one make a copy of your save.
Thanks, Reason I asked was I had been told by a mate it was to do with the friendship ratings. I cant be bothered with them so now I know thats not involved I can sideline that stuff until I have finished the story.