When swapping you only need to tell one player to swap, not both. I do not know though whether it makes a difference if you tell either one or both (for instance, whether you should tell the one with better decisions and teamwork...)
They swap their instructions as well. for instance, if you swap the two wingers, the ML that went to the right wing will come close to throwi-ns from the right not the left.
This can be annoying if you swap a tall and a fast strikers. as the tall will have FWR and RWB sintructions and the fast will have hold up ball and whatever you instruct your targetman. However, the set piece assignments and the playmaking / targetman assignments are not swapped.