The Command that we see in-game is probably the Options guy in the Aquitaine's mainhall.
Dude, they look nothing alike!
I think the whole concept is inconsistent, since our BlackMan appears everywhere. But I think the statement in Battuta's post by 'Command', confirms that he's on Third Fleet HQ ("...This is Third Fleet HQ...").
I Agree with Androgeos. The Options guy and the head ani for "Command" look rather identical.
In the case of "where is he?", then i'd bet he's on the Aquitaine. The headani for 3rd fleet HQ isn't "blackman" but rather is identical to the captain of the trinity/Actium/Colossus/etc... (IIRC the same voice actor does 3rd fleet HQ and the Colossus)
Also, "command" is simply a quick way to say the orders came from higher up, kinda like an Army Company CO who would relay orders to his men would refer to the source as "Battallion", such as: "Battallion wants Baker (as in Baker Company) to take that artillery position and dig in until reinforcements arrive."