Many laws control the conduct of the executive branch
"Attempting to control the conduct of the executive branch" doesn't imply a violation of the constitutional separation of powers. Congress has many laws that control the executive.
- 35 USC 101 tells the Patent and Trademark Office what subject matter is patentable.
- 15 USC 1052 tells the Patent and Trademark Office that it must provide registration unless a trademark falls into one of several categories.
There are many many more.
This power comes from Article 1, Section 8
The power to enact laws that tell the executive branch what to do stems from Article 1, Section 8 of the Constitution, which gives congress the power "to make all laws which shall be necessary and proper for carrying into execution the foregoing powers, and all other powers vested by this Constitution in the government of the United States, or in any department or officer thereof."
Example of intrusion on Executive authority
But, when a statute intrudes on the authority conferred on the Executive by the Constitution, it is not constitutional.
An example where Congress intruded on Executive authority is Zivotofsky v. Kerry, 576 U.S. ___ (2015). The court held that "the power to recognize foreign states resides in the President alone", and that "if Congress could alter the President’s statements on matters of recognition or force him to contradict them, Congress in effect would exercise the recognition power. An exclusive Presidential power disables the Congress from acting upon the subject." (Citing Youngstown Sheet & Tube Co. v. Sawyer, 343 U.S. 579 (1952), an important separation of powers case that went the other way: the Executive issued an order that infringed on the law-making powers vested in Congress.)
Executive acknowledges that Congress can control how vacancies are filled
There is a case before the Supreme Court in October term 2016, where the Executive is defending its interpretation of a statute that concerns how particular executive employees are hired, fired, or directed: National Labor Relations Board v. SW General, Inc.. The Executive is not challenging the constitutionality of the statute, though. The Executive even argues, basically, "If Congress wanted to control us, it has the ability to and knows how to control us.. it just didn't in this case."
No bills of attainder
United States v. Lovett 328 U.S. 303 (1946) is another case where Congress went too far. The background here was that Congress passed a law that said "no salary or other compensation shall be paid to certain employees of the Government (specified by name)". The court held that: "Legislative acts, no matter what their form, that apply either to named individuals or to easily ascertainable members of a group in such a way as to inflict punishment on them without a judicial trial, are bills of attainder prohibited by the Constitution."
This principle was refined in Nixon v. Administrator of General Services, 433 U.S. 425 (1977). The court upheld an act that directed "the Administrator of GSA to take custody of appellant's Presidential materials". Even given this specific direction to take a particular action, the court found that "the Act does not, on its face, violate the principle of separation of powers."