I have a PC that wanted to run one and I was able to work it into our campaign.
I haven't got all of the meat of it yet, but this is how I run and view the CC.
They operate as an Intelligence service for the Sector Governor. Due to the Tranch Incident they are limited to non-active War zones and thier authority is limited to PDF and non-active IGunits. This doesn't mean they are completely helpless. They have all of the authority of a real Commissar and thier limitations. They are not in the Chain-of-Command of units, but can execute soldiers.
They operate in a heirarchy system with it's internal CoC. They are all equal to one and other, but depending on what office you hold and what that means would determine the authority you have over the other CC's. Sort of like the U.S. Congress. When they go out into the field they may be assigned to a unit or sent out as a independent group with one of their number being the Officer In Charge (OIC). How and what they do would be determined by the mission they are on and what the OIC decides.
With exeption of heavy vehicles and armed regiments, they have everything they need to operate indepently from the rest of the Imperium. This includes administrative, medical, supply, forensics and investgative staffs. Thay usually operate as loners or up to groups of 25.
They are extremely secrective and suspicious of everyone and therefore damn near hard to infilltrate. There is no know pattern to thier recruitment styles as theycome from all walks of life. My PC's found a man that was recruited and before he shipped off, killed him and replaced him with one of thier own.
I modled them after the German SS and KGB if that helps.
I'm still fleshing it out, but so long as the Commissariat or anybody else doesn't mind they have free reign on a planet. This is especially true on the capital planet where they enjoy equal footing with the rest of the Imperial Agencies