They may be running things, but ultimately they answer to the top. For example, if the head of an organization says that the organization will be affirmative action friendly, and all decisions in that regard must be referred to the top, it will happen. Of course the President will not know every single policy decision in every agency, (hopefully no one is that much of a micromanager) but the tone of the administrattion will be set, and those that don't fit in or respect that tone face the possiblity of losing their job, being reprimanded, or being mis-assigned. At least that's the way it works at state level in NYS. I would assume federal isn't any different.