For example, the President could fire the Secretary of Labor at any time, for any purpose, because executive department heads serve "at the pleasure of the President." The same is not true for FTC commissioners, who are statutorily protected from firing except for "inefficiency, neglect of duty, or malfeasance in office." SCOTUS held in Humphrey's Executor v. United States (1935) that an FTC commissioner could not be removed by the President for policy reasons, because it was explicitly granted non-executive powers by Congress.
His power to issue Executive Orders to independent agencies is unclear, and often Presidents will "recommend" they do things, rather than "direct" them, as he would an executive department.