Well, here's how MY Cobra Hierarchy works;

Cobra Commander (Supreme Leader)
__________________________________________________ _______________


Colonel Vargas Cobra generals Crimson Twins
| | |
Shadow Guard Neo Vipers Crimson Guard Commanders
| |
Ninja Vipers__Specialist Vipers Crimson Guard Immortals
(Techno,frag,etc) |
| Crimson Guards
|
|
Vipers (Viper Corps)_______CLAWS
|
|
Night Watch/Blue Shirts____V-Troopers (razor,sand Scorp)
|
Toxo Vipers
|
BATS


The Shadow Guard and Crimson Guard report to Cobra Commander directly. The other units are part of the Cobra Army group. Each group has it's own officers and NCO's that report to the cobra generals. Even though the skill levels are different, no unit has command authority over a lower. Each command is independant. Blue Shirt Commanders report to the Cobra Generals just as Alley Viper Platoons. This keeps Cobra segmented and it's harder to organize a rebellion. The Air and sea Corps fall under another Branch and are commanded by a Cobra Air General and a Cobra Admiral. Dreadnoks, Mercs (Skull Squad,etc.) and other independant units are tacked into the Army group and receive orders from either the Cobra General or Cobra Commander himself. (For Example, Major Bludd may be tasked to be a General, so Skull Squad would fall under him at the top. However another mission may have him doing "black Ops" and he would fall in around the Viper Corps level and take orders from a General)

Any questions on how mine works or even a "Well, how about if....." I'll be more than happy to answer!