My main Cobra Command circle is pretty much as you described them: Cobra Commander, Destro, and Baroness form the top tier. Below them are Cesspool, Dr. Mindbender, Scrap-Iron, Slice, and Dice. Major Bludd, Firefly, and Zartan & the Dreadnoks are just independent contractors in my world (though they do most of their work for Cobra). Also, Storm Shadow is a Joe as far as I'm concerned. I don't really see Scalpal as a "main" Cobra. I just use him as the head Medi-Viper.

Now, here's a little secret: I don't really like Mindbender or Zartan all that much. I use them to fill the roles that only they can fill, but that's pretty much it. I never go out of my way to use them when they aren't needed. That's why they're pretty much the only classic Cobra characters who aren't appearing in my crossover (besides Storm Shadow, who as I said I use as a Joe).