No, Congress can't tell the executive whom to arrest or where to position troops or which lines to surveil. Those are executive decisions. It can, however, limit the scope of action of his agencies to what Congress decides is necessary for him to do his job. Congress gave him these agencies, and Congress can limit what it gives to him.
And the "checks" that you mention are utterly unrealistic. Making a choice between not having the ability to defend ourselves at all and living with presidential abuses of power is not a "check"; it's a joke. And talking about impeachment merely begs the question. Impeachment is for violations of the law, but if Congress can't pass a law regulating him, there's no law for him to violate.
You are giving your opinion, based on literally nothing. There is no presidential abuse of power. You have bought into the notion that our civil liberties are endangered by the president exercising his legitimate power. You seem to think that without the courts and Congress interceding, we are endangered. Simply not true. The president, in this case, is free to intercept enemy communications, just as he is free to kill the enemy, to destroy their cities, to blow up their homes, etc. -- all the things that occur during war. You want judicial review? The courts have ruled exactly as I have said. You want some history? Every president has viewed and exercised his power this way, and Congress, until now, has concurred. Now, apart from your opinion and fears, how about some history or something else?
Congress doesn't give the president his commander-in-chief authority. The Constitution does. Once war is declared, in two joint resolutions, the president exercises his constitutional power. You confuse this explicit constitutional power with the creation of executive branch agencies. They are not explicitly provided for in the Constitution. Apples and oranges. This is the problem. You and many others are searching for arguments to support your fears. I don't accept your fears, and your arguments aren't based on any historical or legal substance.
...Or Treason (disloyalty). ...Or Misdemeanor (bad attitude).