The old Marvel comics made the Cobra "ranking structure" much more clear.
Cobra Commander - Supreme leader/ Dictator
Baroness - 2nd in command
Destro - Contracted Weapons supplier, and designer. Occasional Mercenary. Frequent Military Advisor due to his own personal military background expierence. Completely outside the cobra power structure.
Stormshadow - Cobra Commander's Bodyguard. Completely outside the Cobra Power structure.
Tomax and Xamot - Leaders of the Crimson Guard. Akin to a General. Also head of the "buisness side" of Cobra. this includes money laundering.
Firefly - Mercenary. frequently hired, but completely outside the Cobra Power structure
Zartan - Mercenary. frequently hired, but completely outside the Cobra Power structure
Major Bludd - Mercenary. frequently hired, but completely outside the Cobra Power structure, But Frequently put in charge of cobra troops.
In fact, during the Cobra Civil War ( which ended when Zartan kills Serpentor, for the record), destro takes his private army, the Iron Grenadiers, and invades Cobra Island. setting up on the beach.. gets a lawnchair, and a drink with a tiny umbrella, and simply watches the crazy. He and his forces ONLY intervene to rescue the Baroness, whom he then takes with him as he leaves, going back to Scotland.