From War on the Rocks:

These high-level principles, however, do not tell the full story about the complexity of civil-military relations on a month-to-month or year-to-year basis. Both Congress and the courts have significant roles in shaping defense policy through substantive statutes, appropriations acts, and judicial orders, but these are of little direct concern to the rank and file. Civilian control of the military is, as a practical matter, exercised through the chain of command, which runs to the president as commander-in-chief. Neither laws nor court decisions are self-executing. Until the Office of the Secretary of Defense and the Joint Chiefs of Staff turn Congress’s will or a court’s mandate into policy orders, they have little direct effect.