I realize that a civil war soldier would carry a cap pouch and cartridge box for reloading his musket but where would a (Confederate) soldier carry extra black powder and extra balls for a pistol? I have never seen a offical civil war powder flask or bag for lead balls.

Is that why so many soldiers carried two or three pistols? In combat close enough that a pistol would be effective, there would not be time to reload and no need to carry extra powder and balls for a pistol.