The Cargomaster is a high Atha'an Miere position in the chain of command. The position is always held by a man who is often married to the Sailmistress.
The Cargomaster is in charge of the defense of the ship, as well as all trade. His word in matters of negotiations and combat are first and foremost.
While the Cargomaster technically stands below the Sailmistress, she cannot command him when it comes to these matters of his position any more than he can command her where to sail.