I’ve begun reading Forrestor again, and The Commodore causes me to ask:
Must the Commodore be Senior to the Captains serving under him?
Does the Commodore give commands concerning the navigation of the Flagship, or does he makes his desires know to the Captain who in turn gives the orders?
[QUOTE=carnivorousplant]
Must the Commodore be Senior to the Captains serving under him?
[/QUOTE]
Yes.
The Commodore is supposed to treat the captain of the flagship in the same way as he does the captains of other vessels in the squadron. So, for example, the Commodore would give orders for the squadron to proceed to Gibralter, but it falls to the captain to give the orders that cause the flagship to get there.
Human nature being what it is, this scheme was not always perfectly observed. It can be hard for a Commodore to avoid giving hints as to how he’d like to see the ship run, and hard for the captain to resist picking up on such hints (or perhaps resenting them).
Also, note that it’s Forester (which was not the author’s true name).
[QUOTE=Xema]
(which was not the author’s true name).
[/QUOTE]
Well, yeah, but the Brits do that for taxes and stuff. 
It’s too complicated for my poor brain, but I remember reading something on this in Wikipedia.
If I can find it, I’ll post the entry. I am not knowledgeable on this, personally.
Ah! Found it before the edit deadline, even..
Part of it is:
[quote=]
The appointment of Commodore dates to the mid-17th century: it was first used in the time of William III. There was a need for officers to command squadrons, but it was not deemed desirable to create new admirals (as Post-Captains were promoted to Rear-Admiral in order of seniority). Captains assigned squadron command were given the title of Commodore, but it was not an actual rank. The officer so designated kept his place on the list of Captains. In 1748 it was established that Captains serving as Commodores were equal to Brigadier-Generals in the Army.
Commodores could revert to the rank of Captain at the end of their posting (and Captains could be promoted directly to Rear-Admiral without ever having served as a Commodore).
The Royal Navy Commodore was eventually split into two classes. Those of the first class had a Captain under them to command their ship and were allocated one-eighth of all prize money earned by ships under their command. Those of the second class commanded their own ship as well as the squadron. In 1783, Commodores of the first class were allowed to wear the uniform of a Rear-Admiral, a distinction which continued with some variation until the two classes of Commodore were consolidated in 1958.
…
[/quote]
The rest may be found here.
From my experience in the modern [Canadian, not Royal] Navy, a squadron commander explicitly did not command his flag vessel directly. As LiveOnAPlane cites, we were taught that traditionally some squadron commanders were also Captain of their own ships, but that ceased to be feasible with modern communications and tactics (battle commanders became more and more interactive during the course of an engagement, rather than just setting tactics at the outset). The Canadian Navy traces its heritage to the Royal Navy in a more direct fashion than the USN, but wasn’t formed until 1910, and thus was essentially created as a modern Navy.
What LiveOnAPlane quotes corresponds with my memories of Patrick O’Brien’s Jack Audrey books. In *The Mauritius Command * Jack is appointed as a Commodore of a small squadron (appointed over more senior Captains) but he does not have flag Captain to command the flag ship - he does that himself. Later in the series, in The Commodore, he commands a larger squadron and has a Post Captain to command the flag ship.