The EC2000 and older BattleSets each have a database of platforms embedded right in the BattleSet files (i.e. hdsh.res has map, scenarios, database, ...). The CommonDB BattleSets are EC2003 and newer with the exception of the re-done USNI BattleSet (the USNI with the pretty map), and any BS Builder created BattleSet that has an embedded DB.
It is called Commondb since that commondb.res and commondb.rsr pair applies to more than one BattleSet. In practice that means you want to make sure to match up the scenario with the BattleSet. For any of the stock scenarios, use HCDB (not HCDB2). You can always find it in the commondb.bak directory. There are lots of ways for you to juggle the various CommonDB databases. You can save them to sub-folders and swap the correct one into the main game folder before you start the game or you can use the HC Launcher and point it to the correct DB or you can download the right DB each time you play. Etc. Etc. Etc.