Flying Colors is both the name of a series of Age of Sail naval wargames, and the first title in the series. Designer Mike Nagel self-published the system before it was picked up by GMT Games in 2005.
The system has slowly become more flexible, as it now covers both fleet actions and duels (with slightly different rules between the two). Damage and the like can be kept track of with pen-and-paper, but I've found the markers are just fine.
Board Game Geek
Flying Colors Playbook
Ship of the Line Playbook
Serpents of the Seas Playbook
Blue Cross, White Ensign Playbook