Final Cut Pro and Mac OS X know how to manage media. Once you import a source file into Final Cut Pro, best practice is to not alter the file in the Finder. If you decide not to copy files into Events during import, then you must exercise strong self-discipline to organize source files before importing.
Final Cut Pro manages Events and projects separately. These are encapsulated within two folders in the ~/Movies folder, by default, or at the root level of a secondary hard drive.
The File menu has several commands available when an Event is selected.
You can drag a clip or ...