All characters have 12 Die that they can assign in the following manners. FIRST, you must bring your stats up from those of a Line Commando to the branch you want. If you want to stay in the Line, fine. Then you can do with the remainder as you wish. If you wish to improve attributes, you may do so at 1D per pip of attribute die, and no attributes may be above 4D. Skills are assigned with 1D equaling 1D of skill dice, and 1D equaling 3D of specialization dice.
Go through the ImpSB. If you have the dice, you can be from any of the listed branches of the Imperial Army and Navy, including the Pilot Corp. This is because some Storm Troopers are drawn from regular ranks. The only thing you won't be able to do is the Royal Guard and the Space troopers. Anything else, so long as you have the free dice, is fair game.
I'd give the characters 1 Force Point, or 2 Force Points and a Dark Side Point and 5+1D Character Points. This is because they are veteran, elite troops.
With the SC's, I figure that you will use regular character names and background, but with a very pro New Order slant. Your kit is stock, with heavy weapons and electronics being issued per mission. I'd give you 500cr in savings, which you can spend however, or you can pocket it. I figure a Storm Commando makes 100cr/month, room, board, armor, ammo, medical and all the New Order propaganda he can stomach.
As for how to run the campaign, play it like a regular, Rebel SpecOps unit. Get in, do the deed and get out. We never heard of you if you screw up. The big difference is that the Empire will raze the area where you screwed up with orbital fire support, to make sure that there is no evidence.