A fairly streamlined command structure works for me; CC in overall command, Major Bludd as Infantry commander, Copperhead as Naval commander and Interrogator as commander of Cobra's air force. The Baroness is head of intelligence and Destro is not part of Cobra at all (in my Joeverse he is with MARS which is separate from Cobra). The next level down, (Firefly, Zartan, etc), are in charge of particular types of troops within a branch of service.