Please see the Database Management & Maintenance Guide for general database information.
The PokerTracker 3 database was designed to handle millions of hands so there is no need to create multiple databases for different sites, limits, etc. One large database should be all that is required. The only time that a second database would be needed is if you opt to store observed hand histories in one database and played hands in another database.
This tutorial describes one way of managing observed hand databases should you feel the need to use more than one database.
This method uses a single database for your 'played' hands and multiple databases for 'observed' hands, each of which is used to import hands for an amount of time before creating the next database. The HUD is configured to use just the last few observed databases.
The advantages of this method are to keep your 'played' database fairly small (meaning quicker reports, analysis of results, housekeeping, etc) and allowing older observed hands to be ignored (by the HUD) once you judge that they are out of date and therefore no longer useful. The older observed hands [databases] can either be kept for reference or deleted.
Note: to create new databases you need to be registered - you cannot do this if you are using the free trial.