Profession (Sailor/Sailing) for out of combat travel, which you could argue would encompass navigation as well. Survival would help to avoid being lost using stars and such but I could also see that covered under the Profession skill function.
Skull and Shackles part 3 has this for plotting a course:
Navigating a ship requires a successful DC 18 Profession
(sailor) or Survival check. Characters with at least 5 ranks in Knowledge (geography) or Knowledge (local) gain a +2 bonus on the check. Attempts to navigate without proper navigational tools (such as an astrolabe, charts, compass, or sextant) take a –4 penalty on the check. Success means the ship reaches its destination as planned in the normal time.
A failure means the ship gets lost, following the rules for
getting lost on pages 424–425 of the Core Rulebook. Each
failed check adds 1d4 days to the ship’s travel time.
Skull and Shackles players guide has this out of combat ship travel:
Prof Sailior Check
Outside of combat, the base DC for all sailing checks is DC 5.
So first plot a course as navigating above then each day or however much you feel a DC 5 Prof sailor check.
If the DC seems to simple just make it harder I guess, maybe alter it for weather and wind speeds maybe.
In the vehicle section at the SRD you can see which vehicle is used with which skill.
For example the longship: Driving Check Diplomacy or Intimidate while rowed, or Profession (sailor) or Knowledge (nature) +10 to the DC when sail is used.
Profession (sailor) or knowledge (nature) is used for most sailing craft.
Pretty vauge, I would say 1 per day and 1 per night if travelling for 24 hours maybe. It's also not mentioned (as far as I can see) what happens when you fail the roll. Maybe just add another day on to the ships travel or just follow the lost rules maybe?