I don't know if a concrete command structure has ever been laid down. That's one of the facets of the series that feels like JMS just made it up as he went along.
We know a certain Captain was promoted to Colonel after season five. And we know another character went from Lieutenant Commander to Commander to Captain. Somehow Generals fit into that. And there's always Lieutenant Corwin, who seemed to be at the bottom of the barrel rank-wise (didn't we see him get promoted during the series--what rank did he originate?).
EDIT: Well here are a couple of possible explanations: