It is perfectly clear and incontrovertible that the President is in charge of what goes on in the Executive Branch. The Constitution says so.
How the government keeps secrets is a matter that is primarily regulated by a series of Executive Orders. In short, the “need to know” is based on a Presidential order, and as the chief executive, there is no higher authority in government on who can determine need to know. All classification authority derives from the President, so barring a “can God make a burrito so big that He cannot eat it” type of metaphysical question, of course the President is entitled to knowledge of all classified information.