In this case, President Andrew Johnson had to issue orders to the commanders of the Southern military districts through the General of the Army. The man holding this position at the time was Ulysses S. Grant.
This law was passed by the US Congress due to their fear of Andrew Johnson not following through on the efforts of Reconstruction in the South after the Civil War. Northern politicians knew that Andrew Johnson himself was a Southerner and was very lenient when allowing them back into the United States. To ensure that these states continued to follow the orders of Congress, they had to implement a law that would allow someone else to have power over Reconstruction. That man was Ulysses S Grant, a former military commander of the Union Army.
To transport troops, destroy others naval superiority, and to trade, they were able to destroy the enemies vital supplies and they were able to be sunk easily.