Every soldier in the United States military has a distinct chain of command that he must know and follow. This chain of command is defined by the Goldwater-Nichols Act of 1986. All decisions are expected to be made at the lowest level possible, but if required, can be taken all the way up the chain to the Commander in Chief. To get a job done, you must pass information up the chain where decisions are made. Once decisions are made, orders are given, and the duties are carried out by those lower in the chain. Below is a top-down summary of hierarchy as used in the military branches of the US.
Supplimenting the official military chain of command are some administrative bodies and positions which are not actually part of any soldier's chain of command. Regardless of this, any major military action will be coordinated through the following:
National Security Council (NSC) - this council is a meeting of the minds consisting of the President, Vice President, Secretary of State, and Secretary of Defense. While not members of this council, other possible attendees are the Chairman of the Joint Chiefs of Staff (primary military advisor), CIA officials (intelligence advisors), the Secretary of the Treasury, US representative to the United Nations, the Assistant to the President for National Security Affairs, the Assistant to the President for Economic Policy, the President's Chief of Staff, the Attorney General, as well as any number of other officials that may be invited. The council serves as the principle forum for discussing national security issues that require presidential intervention.
The NSC would fall between the Secretary of Defense and the Secretaries of the Military Departments in order of precedence.
Chairman of the Joint Chiefs of Staff - the principal military advisor to the President, Secretary of Defense, and National Security Council. Appointed by the President and confirmed by the Senate for extendable 2 year terms.
The Chairman would fall between the Secretaries of the Military Departments and the Joint Chiefs of Staff in order of precedence.