Each connected water or land plot (i.e. a unit in that plot could in theory move to the connected plot - ignoring impassable terrain) will belong to the same area. In other words all land plots on a continent have the same area id. All separate bodies of water will also have their own area id.
The game actual tracks quite a bit by area, including how many cities, units each player has, each area has an AI type, how many free specialists each player has (think Statue of Liberty), etc... It is how the Great Wall works, and why it doesn't keep out Barb galleys (because they are in a different area, being at sea).
The areas are computed using the pathfinder routines. You can actually use similar techniques to the way the game calculates them to further break down areas into passable and impassable regions, and even into irrigatable and non-irrigatable regions.
Out of curiosity, what were you looking for it to do for your mod?