If the 'Adjust Qualifying Tables Limits' option is enabled on the Auto Import tab then this setting will be used so that short-handed tables can be recognized. The processed files will not be moved (as they are with Auto Import). To change the Active database use the menu Database > Set Active Database. Manual Import will always import into the current Active database, as shown in the title bar of PT3. Manual Import is much faster than auto import for bulk imports if you have a lot of hand histories to import all at once.
If you want to import hands while you play and use the HUD then you should use the Auto Import tab.
The Manual Import tab is used to import a large number of hands while not playing for instance when creating a new database or after a datamining session.