The Navigation Order is one of the three standard orders that players can use on their turn. Using a Navigation Order generates one navigation point by default, plus an extra navigation point for each Crew member that is manning Navigation Nodes in the On Deck area of the player's ship.
Navigation points can be spent on three things:
Each of the above actions normally cost one point navigation point, but if a ship movement starts or ends on a Rough Seas space, navigation actions cost two navigation points each (noted on page 23 in the rulebook).
If a ship starts its movement on a space covered by a Storm, it has the same navigation cost penalties as for Rough Seas, but with the additional penalty that each action that changes the ships orientation causes 1 Damage to the ship.
If you for some reason have more navigation points than you want to use, you don't have to use all of them. But you can't save them for later -- if you don't use them before finishing the Navigation action, any unused navigation points are lost. In particular, you can't stop in the middle of the Navigation action to do other actions on hexes that you pass. If you want to perform an action on a hex, your ship has to stop on that hex, not just pass it.
When moving, you can't end your movement on an occupied space, but one player ship can sail through a space occupied by another player ship, as long as it has enough movement points to move to an unoccupied space before it ends its movement. (The rulebook isn't clear about this, but an official answer was posted about it.)
Note: if you have a Crew member with the WAYFINDER Trait, you may explore new hexes without needing a Crew member manning the Crow's Nest Node, and without spending navigation points.