As sailors, you are afforded a lot of downtime beyond the trappings of civilization. Most career privateers develops some sort of hobby or project to keep themselves busy. This can be as simple as carving scrimshaw or as complicated as learning a spell. Once per sailing week each member of the party (usually) has one free day. If you Go Through the Motions in your ship duties you can squeeze in an extra day off.

Official Pathfinder Activities

Bribe a Contact Offer a bribe to your contact to help your criminal activities in some way. This may require you to be in port.
Craft Create, repair, or improve an item in some way.
Create Forgery Create a forged document.
Deconstruct Take an item apart to learn how it works. You will need equipment appropriate to the item type.
Gossip Seek out rumor's about a target. This may require you to be in port.
Grow Grow an item from a living thing.
Learn Name Spend a week trying to discover and learn a creature's name.
Longterm Rest SLEEP IT OFF.
Retraining Change a character decision.
Secure Disguises Procure or create disguises.
Treat Disease Spend time treating a disease to give a bonus to saving throws.

Home Brew

Cartography/Research Spend time studying and learning from maps, books and logs.