You can only have 1 flagship, that ship picked must first must be in a fleet and cannot be removed from said fleet after being a flagship.
It cost 50 credit to set a ship as a flagship and you cannot change to another ship unless the flagship is lost (Sink/plundered) for 7 days or more. (You can get back the flagship if you take it back from the sea or someone in those 7 days.)
The fleet will have a flag next to on the plunder board. Which ship is the flagship is unknown.
Flagship's max attribute for all 6 is doubled (10 to 20 max, points gained from leveling is still the same)
Flagship gain 2 extra traits based on it's ship group.
Howker - Galleon
(Aggressive Tactics - Gain 8 extra guns and fleet ships deals 10% more damage.)
(Careful Tactics - Gain 150 more hitpoints and fleet gains extra 20% chance to avoid a skirmish.)
Large Fluyt - Brig
(Hit and Run - Fleet gains 4 danger per battle instead of 6.) [8 instead of 12 with Hostile Waters]
(On The Sidelines - Entering a port no longer gives danger.) [Hostile Natives still works, similar to having permanent treasure fleet on 1 fleet]
Brig of War - Ship of the Line
(Raid The Coffers! - On attack victory, gain 20% extra gold.) [Money taken from the defender]
(Advanced Logistics - All ships on fleet gain 50% more cargo space.) [Extra Cargo trait also gains the bonus]
Man of War
(Offender - When winning a battle and the enemy's ship loses a level, it lose 1 more level.) [Gain money from that lost level as well.]
(Defender - Ships in this fleet can't be unleveled from losing battles.)
Bonus Double and traits disappears after being lost. (Stop being a flagship.)
(The bonus points put into the ship still exist, but the attribute max each will return to being 10 and any extra points will be lowed to 10)
Values can change.
*Shrug*