The Fleet Admiral is the Commanding Officer of the entire Timelords Fleet. Only one Fleet Admiral can be in power at any given time. Pirko is currently serving as Acting Fleet Admiral.
The fleet commander has unlimited command over the fleet. He can start and end wars, promote and demote members and declare any kind of alert without the consent of the admirals. He also has the power of veto, so if he feels that the Admirals' Council is not making the right decision he can stop them from doing it. However, the powers are almost never used.