alt Hacker News> The President is not supposed to directly order the people at these agencies what to do.
The Constitution disagrees with you, since it expressly directs the President to "take Care that the Laws be faithfully executed". It's literally not possible to "take care" of this without issuing orders to that effect.
The clause that you cited does not in any way contradict what I said.
"Independent" agencies are supposed to function with a high level of autonomy. The president does not have to give individual orders to underlings at the DOJ in order to ensure that Congress' wishes are faithfully executed.