Brilliant. I like your designs; they feel much more realistic than a lot of ships out there. Much more self-contained. I love the fact that you've thought everything through a lot better, as well. Makes it all feel more realistic.
There are in fact a series of command centers especially on a ship this large. At the core of the ship are the CICs as you mention. These are where senior weapons and tactical officers coordinate fire control, battle space information and track combat situations. However, the senior officer isn't usually there. Instead, this is where you will usually fine senior commanders (Admirals or Squadron Commodores). The Captain himself is on the bridge which is (if you go to the large view) located just forward of the forward underbelly turret. Here, the Skipper gets a command view of the battle-space (protected by some of the heaviest shields on the ship) and can keep his attention on ship action and direction firing missions with the senior weapons officers located there (who take info from the CIC and turn it into fire control information for the main guns, missiles, point defenses, etc).