When the president issues a rule or regulation that reorganizes or otherwise directs the affairs of the executive branch?

What you described is called an executive order. The president can do this whenever he wants and if it's unconstitutional then the congress and the judiciary system, more specific the Supreme Court, can overthrow this and ban the executive order because it's considered to be unconstitutional or harmful. The president can use this for almost anything.

This is known as "The President's Choice". It is when he makes a military decision that he thinks would be best for the country.