If a ship has surrendered and isn't sinking, you can take it after the battle. You get a results screen and under it will be your ships and below that, any of the enemy's ships that you've captured. You need to add those ships to your own fleet for them to become yours, otherwise it is automatically scuppered when you exit the results screen.
Routing ships are a little different. If they escape before the battle ends, you do not have the option of capturing them. You can do two things, sink them before they get away or send a fast ship after them to capture them.
Does that help?
-Love Gaius
TWH Seraph, TWH Grand Zinquisitor & Crazy Gaius the Banstick Kid
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