You generally see Admirals sticking their flags on a cruiser of some description, but then you also have Sisko commanding Operation Return from the Defiant. One assumes that in general you want your primary axis of command to be on the most durable ship in the fleet, and we see a kind of acknowledgement of this in the beta-canon Federation-class dreadnought. Which is just a Constitution with an extra nacelle and more specific CnC/support functions. We also see battle and strategic planning taking place before battle is joined, and we have Dukat dictating major fleet maneuvers from a post behind the lines in Operation Return. But when battle is joined, any large organisation seems to break down.
We do get a hint of continual battle organisation in the Battle of Sector 001, where Starfleet is using 'mobile positions' to direct starship maneuvers. One assumes these mobile positions were in relation to the Borg Cube and were probably specifically anti-Borg tactics with trying to rotate ships out of the line of fire before they can be destroyed by the Cube. But at a certain point with the sheer technological sophistication of starships, command and control probably becomes a function of the software rather than the hardware and any ship can do it.
