When is the president put in charge of the military as Commander in Chief hmmm? Where is that in the Constitution?
When the Congress of the US authorizes use of force OR when we are attacked. Get it? You are in way over your head.
Article II
Section 2
The President shall be Commander in Chief of the Army and Navy of the United States, and of the Militia of the several States, when called into the actual Service of the United States; he may require the Opinion, in writing, of the principal Officer in each of the executive Departments, upon any Subject relating to the Duties of their respective Offices, and he shall have Power to grant Reprieves and Pardons for Offences against the United States, except in Cases of Impeachment.
The only qualifier that I see is that the President is not in command of the militia unless they are called to the service of the national government.