Anyway back to the main point, the XO / First Officer / Number One etc isn't going to be in his bunk during a battle because it's not his shift - "All hands on deck" etc.
Correct. The XO will be on the Bridge with the CO.
A good reference for this might be MgT: Secgtor Fleet by MJD.
In particular (MgT Sector Fleet, p.74-75):
Command Procedures
Command of a vessel rests with the Captain (whatever his actual rank). The Captain issues orders as to what is to be done. The Executive Officer then ensures those orders are obeyed, or finds out why not. If the Exec does not inform the Captain that an order has not been carried out, the Captain will usually assume that it has been obeyed.
Department heads make specific decisions as to how to implement the Captain’s orders, and pass those orders down the chain of command to their subordinates. For example; the strike cruiser Seydlitz is taking a pounding from system defenses. The Captain decides she cannot complete her mission and needs to escape quickly to avoid destruction. He orders the Exec implement an emergency Jump procedure. The Exec orders the Astrogator and the Engineering Officer to prepare for crash-Jump. The Astrogator calls up a pre-prepared course plan. The Engineer orders his Power and Jump chiefs to implement certain procedures. They do so, using their initiative to deal with any glitches or problems they encounter. This may require hands-on work, or orders to their team. Meanwhile the Chief Engineer monitors both procedures, offering advice and guidance to both teams to ensure a fast, efficient procedure that gets the drive ready in minimum time.
Neither the Power or the Jump chief is totally happy with what he has achieved, but the Engineer decides on the best compromise and implements it. He has reservations, but knows how urgent things are. Having achieved the best Jump configuration he can in the time available, he tells the Exec that the drive is ready, but that implementing now carries a significant risk of Misjump. The Exec at this point already has confirmation from the Astrogator that Jump is laid in. “Emergency Jump ready, Captain,” says the Exec. “Chief Engineer has reservations.”
The Captain weighs the situation… risk Misjump now, or take more time to prepare and suffer more damage? “Execute Emergency Jump!” says the Captain, and the Astrogator, not waiting for a repeat from the Exec, does so.
This is standard command procedure. The Captain is not interested in specific details. He must weigh the issues – his own appraisal of the tactical situation, the engineer’s reservations, the fact that the Astrogator did not mention any reason why the ship could not Jump safely. His decision is based on the overall situation. Subordinates must take care of the details, the Exec must filter and distil the information for him, and he alone must take responsibility for the final decision.