On the beginning:
you need to roll for leadership for all vessels with or without admiral/commander. Why? In case of "Bridge Smashed" critical hit the commander is gone and the vessel uses its rolled for leadership.
So, Whiro, regardless of what comes next: you MUST always roll for leadership for a vessel with or without commander on it.
On placement in general with the most basic fleets:
Chaos must place its warmaster on the biggest ship.
Imperial Navy wherever the player wants.
So, eg, using Chaos the placement is first, then the dice will be rolled. So, to keep the mechanic flowing the same applies to the lesser Chaos commanders which can be used: pick ship, then roll. The roll could be higher, pity that, but a lunatic Chaos captain would just kick the smarter subcommander out of the ship if he starts a mutiny (or something like that) if the bridge is smashed, the smarter crew takes over. lol.
Now, Imperial Navy. You may place the admiral on any vessel (though generally speaking he will be on the Battleship if present but is not a rule to do so!). So if you rolled for leadership and you roll good and roll the highest leadership for Battleships, battlecruisers and cruisers but a small Endeavour light cruiser would get Ld6.
Would you place your Leadership 8 admiral which you bought on the Endeavour with Ld6 or on the Emperor with Ld9?
To avoid quirky ideas like that we go with Chaos:
pick admirals, captains, etc. Place them on a ship. And the roll for leadership.
Except the Cadia things as Xca|iber points out.