The military commanders at Southern Command are constantly referred to the Joint Chiefs of Staff by the president, other military officers, and Gran Colombian militants. At the beginning of the thief and these individuals are based in the Southern Command in order to oversee the rebuilding of the US naval fleet. The Southern Command also acts as a new Pentagon/headquarters for the US military during the rebuilding of the fleet and the war against the Gran Colombian Empire. Any other discrepancies in their positions can be attributed to new procedures in a post-red flue world. In the show, the government has been relocated and the military is shown to be smaller so it would also be logical to assume there are minor changes in the roles that the Joint Chiefs of Staff have.