The squadron and signals

Every ship on your side with an NPC captain is in your squadron, and you are its flagship. Until you make a signal, each fights as it would alone.

Four ships flying the Crown's ensign in a column, seen from astern of the last; the two nearest are still settling into place. — The squadron coming into line astern behind the flagship, having come down from windward.

Making a signal

Tab opens the signal list. The battle doesn't pause. Choose with the up and down arrows and make the signal with Enter, or click it, which also closes the list; Tab, Esc or a click on the sea closes it. While it's open, A, D, W and S still steer and set sail, and the yard and gun keys still work.

There are six signals. Each goes to the whole squadron.

Line abreast to starboard, line abreast to port, line ahead and line astern each give every ship a station beside, ahead of or behind you, at equal intervals, the ship nearest you when you made the signal taking the nearest station. In line, a ship keeps station and fires as its guns bear, but doesn't manoeuvre for a shot.
Engage at will releases the squadron to fight freely.
Heave to: each ship lies to where she is, sails in, and fires as her guns bear.

Signals take time

Each ship answers after a delay that grows with her distance from you, wherever she is: nothing blocks a signal. She obeys as she answers. The signal list shows how many ships have answered, and each answering ship's label says so.

The flags

Your ship flies the signal in force from the lee end of her main yard, and each ship repeats it once she has answered, so you can see who has the signal. Every line signal has a white cross on blue on top, for "form line", and beneath it the line: plain yellow for abreast to starboard, quartered blue and yellow for abreast to port, yellow over blue for line ahead, blue over yellow for line astern. Engage at will is plain red, alone; heave to is white over red. The signal list shows each hoist beside its name. A struck ship flies none, and a lost signal comes down.

A new signal overtakes the one before it: a ship that hadn't yet answered the old one never will. If your ship strikes, your signal is lost, and the squadron fights on alone.

Keeping station

A ship on station matches your sail. Behind her station she sets more; ahead of it, less. So a ship as fast as yours can't catch up while you're under full sail. Shorten sail and let her come up.

The wind matters here too. A square-rigger can't work up to a station to windward of her, so make a line signal with your squadron to windward of where you want them, or bear away and let them come down to you.