I will probably keep the decision at the personnel level. Why? Because in real life, if you sub in a player any time you have an inside run, your opponents will quickly realize this and exploit it. But if you sub in a player based on formation, that's not telling the defense anything they won't already know when you line up.
Sure, here you don't have the ability to respond on defense like that, but for the sake of realism I have decisions like this happening at the personnel/formation level.