The process works as specified by various presidential executive orders. These are essentially the laws under which national security works.
This is the part that people get wrong. The president as top of the food chain, can issue new executive orders that add to, modify or delete sections of previous executive orders. But once enacted, even the president has to follow the procedures he puts in place.
The best analogy would be if the commissioner of baseball was playing in the major leagues, he could change the rules at any time. Everybody has to play by the rules in effect. But as commissioner he is free to change the rules, but only after the change goes into effect can he play by the new rules.