I've gotten sort of decent at it, when the circle underneath the enemy ship gets green. FIRE. If you want to capture the ships, hammer the hell out of them with chain shot to where their sails are in tatters. When you go to board click the boarding icon then ram the ship, an icon will come up as a countdown as your ship tries to grapple, if the sails are sufficiently wasted the won't be able to escape, and you can capture it.