Considering satellites can get bigger than what a small craft bay can hold, I would say they can definitely be deployed from cargo, as there is no other way to deploy them at that size. Small Craft Bays can only hold units of up to 200 tons, but satellites max out at 300 tons if I remember correctly.
For the C&C overlord:
Personally I would look up how much support staff would be needed to maintain everything it can carry at 100% efficiency, and put that in it, along with enough Comm Equipment to access satellites and do everything else you could use it for. I would probably also put satellite imagers on it, so in the absence of satellites it can fly up there and give those bonuses itself. If possible I would add a grav deck for the C&C bay so they could work as if on the ground, while in orbit providing those bonuses (if they are legal, I can't remember if they are for DropShips or not).
I probably wouldn't put an NCSS on it, because those are primarily useful in space, and this seems meant to command ground forces. If available though, I would include a mobile HPG. If you have extra space, you could go with extra field kitchens and MASH units along with quarters for the crew for them. I'd roll any remaining tonnage into cargo and use that cargo for the C&C role, like having a mobile HQ in storage that could be brought up and readied for use if needed.