Blind hyperbole, right from the beginning. Nowhere in Will's column is there anything about "micromanaging". What it does say is that Congress plainly has the power to ensure that the President's surveillance is related to fighting the WOT, and not just a free-for-all for any kind of fishing expedition he wants to go on.
You are so confused. If necessary and proper means what Will says it does, which was explicitly rejected by the framers, then of course Congress has the power to micromanage all aspects of the executive. That's the point! As for a check on the president, go back to the Constitution -- Congress can defund the program, it can defund the war, it can impeach ... it has much power. Just not the power to run the executive branch. This isn't a mobocracy or parliamentary system.