[SAMWolf]

If an Admiral has his Flag in a ship, does the Captain still retain command of the ship? Or does the Admiral override his command?

[68-69TonkinGulfYachtClub]

"If an Admiral has his Flag on a ship, does the Captain still retain command of the ship?"

Yes, the Captain is in charge of the ship.
The Admiral on board has control over the task force and then the Captain would take orders
from the Admiral (along with all the other Captains in the group.)
The Captain is always the senior person responsible for the ship.