According to the Starfleet Operations Manual, Fleet Admiral is a rank and a position. The fleets are commanded by a "Fleet Admiral" who ranges in rank from Commodore or Rear Admiral (depending on era of play) to Fleet Admiral. The chain of command then goes down to subordinate Admirals and Captains of the Fleet. Fleets are usually divided into "wings", a Rear Adimral usually commands a wing.
In Kirk's time, Starfleet only had about 350 capital ships, by the 2340s, Starfleet had over 1000, divided into 27 fleets. Before the Dominion War, Starfleet had about 6,100 starships. After it, only about 2,500 in operating condition.
Fleet Admirals can do practically anything they want, within regulations to carry out their duty. Rarely do Admirals break the "regs" such as Admiral Leyton's attempted coup on Terra.
As far as charges go, small offenses are handled "in-house" which usually take the form of a verbal dressing-down, a reprimand, loss of privileges, or brig time.
Bigger offenses usually result in a Board of Inquiry, usually a panel of field officers will sit in judgement of serious, but non-criminal, offenses. There is also a BOI in the case of a Captain losing his command, such as when Picard lost the STARGAZER.
Criminal offenses, murder and mutiny, etc... will result in a Court Martial. Usually the worst that can happen is being sent to a penal colony, only General Order Seven (Capt. Pike's order to never visit Talos) carries the death penalty. Court Martials of senior officers are exceedingly rare; the first court martial of a serving captain occured in 2267, when Captain James T. Kirk was tried for causing the death of Lt. Cmdr. Ben Finney.
"Retreat?! Hell, we just got here!", annonymous American Marine, WWI
"Gravity is a harsh mistress....", The Tick