(Clearly I should look into the math before spouting numbers.)
The Admiral commands the fleet personnel aboard, not the troops aboard the ship. THE CREW MEMBERS ARE MOSTLY TECHNICAL CREW, WITH THE MARINES/BAORDERS FALLING UNDER GAR.
Orders to the men: BCMD > Admiral
Orders to fleet personnel: BCMD < Admiral
Looked up some math around here, http://starwars.wikia.com/wiki/Grand_Army_of_the_Republic/Legends , and determined that the Marshal Commander has somewhere around 589,824 - 1,120,000 men under him.
Another note, each Admiral seemed to be advisors when it came down to the jedi aboard. (Yularen and Anakin for example.)