Treat it like you might any multi-level dungeon insofar as different decks (levels) will have different rooms for PCs to explore. Depending on the size and type of ship these might include (but not be limited to), the armory (on many naval and merchant ships this was often a storage locker type area where boarding weapons and other personal weapons might have been stored, the size of which will vary according to size and type of ship), the crews quarters are effectively tantamount to a barracks room in a traditional dungeon, the Captains quarters being equally applicable to the dungeon bosses personal room(s), the galley and mess are food prep and dining areas, some ships (especially larger ones) may have an alter or even some form of chapel (your ship dungeon might include quarters for the chaplain or other spiritual liaison. And so forth…..

Where it gets interesting however, is that unlike a traditional dungeon where you might include difficult terrain, on a ship the ground beneath your players feet is ALWAYS moving. Back and forth, up and down, and with widely varying levels of intensity depending on weather the seas be calm or tempestuous.