the players preference wont change, for example patrick viera would always have preferred to defend/support along with roy keane regardless of who they played. however it may be best for the team that they attack so make them play differently or pick someone else who will fulfill that role.
one of the greatest developments of the fm series that simply picking the strongest 11 will not guarentee a win, in fact leaving out your best 3 players in some situations will earn you a better result. tough decisions that only the brave/foolish dare to make