Saves.yml is used by default to store all data on created NPCs.
Mouseover to view info:
# Citizens NPC Storage npc: '0': name: My_First_NPC traits: spawned: true type: PLAYER owner: Steve location: world: world x: '92.65002360423462' y: '3.0' z: '-264.5621058817138' yaw: '87.90003967285156' pitch: '21.14999008178711'
Database usage can be configured inside of the config.yml. Database usage requires more setup, but runs quicker when dealing with large numbers of NPCs.
A quote from the config.yml (mouseover to view info):
database: password: username: url: driver:
See also: Configuration