The powers that the President has as commander in chief of the armed forces are not specified in the Constitution. Instead, they have sort of evolved and have been, at times, the subject of a great deal of controversy. For example, President George W. Bush claimed that his power as commander in chief allowed him to do things like wiretapping some American citizens.
There are many powers that the president has that are much less controversial. For example, the President has the right to send troops to anywhere in the world at any time. The president has the power to decide on war strategies as President Roosevelt did when he decided that the US would focus on fighting in Europe first in World War II. The president has the power to order specific actions by the military. For example, President Obama directly ordered the operation that killed Osama bin Laden. Less successfully, President Carter ordered the ill-fated attempt to rescue the hostages in Iran in 1980.
Thus, the president has the power to exercise almost complete control over the operations of the military.