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The flagship is a useful all round ship, with a reasonable speed, good cargo capacity, and deals sufficient damage whilst having enough hitpoints not to be destroyed in your first corsair fight. You either start with this ship (selected in continuous mode options) or you buy it from Lord Northbough when you house citizens. This ship also has the added advantage of having two up upgrade sockets. It also has no upkeep cost, so can be a good ship for no cost.

Early in game it is a quite adequate military ship. It can win against one small military or corsair ship, though barely.

Flagship also can perform early attack or escort missions. Trick in doing escorts is to attack NPC ships, intercepting your escortee, before they start firing at it. Enemies will not fire back, and you will be able to sink or at least slow them down before they do any harm to quest ship.

Tip: Through the use of boarding parties and letters of marque (unless you are at war), you can obtain an infinite supply of maintenance free flagships from your opponents. If you can afford the corsairs cost early game you can stock up on boarding items and quickly build up your free navy. If you wait until after you've allied with corsairs (could be hours into the game) you should have some stronger ships to help with acquiring flagships.

When you're at war with an AI, sit your main boarding ship near Northbough and find your enemies flagship and sink it. With luck the AI will strike first making it easier to get your first ship. After that just keep boarding and taking over every new flagship that Northbough sells the AI. Any large warship/cog can take a flagship at full health, so try to use them as your main boarding unit.

You will eventually work your way to as many ships as you want. Essentially flagships are more durable small warships, but they are faster, have more item slots and can be upgraded. They can replace small trade vessels, saving you money, not being helpless to corsairs and getting supplies to you faster. In mass numbers, they can be extremely dangerous, especially when upgraded. It takes about 5 flagships to destroy a large warship withouth losing one.

Final Note: This above strategy takes a great deal of time to amass such a large quantity of flagships, mainly due to the fact that the corsairs do not always stock boarding crews. Utilized early however, it can take the place of small trading ships and give you better protection in case an AI declares war on you. If you're the patient type of player, this strategy will save you on production chains and increase your income to focus on military camps.