well dont quote me as saying it would have made a difference, game manual basically says 'coach will do the best to make sure the team wins'.
but im assuming that if your best players have played the whole game up to that point, and reserves will perform better due to stamina, then he will still sub your starting players.
probably something worthwhile checking in the forums actually to see other peoples experiences. Ive never personally used it that much either, so yer, dont quote me!