When you first launch Clipstart, it will prompt you to choose to either "keep references" to added movies, or to copy them to a central location. You can change this setting later by choosing Library from the Window menu.
When keeping a reference to movies, Clipstart stores the file path to the movie file in a file called Movies.db in /Users/your-user/Movies/Clipstart. Clipstart will also use this folder for importing from a camera or SD card.
When copying to a central location, Clipstart stores both the Movies.db file and all the movies and thumbnail previews in the location you specify. This is convenient if you have an external hard drive for storing movies.
Copying files is actually a two-step process. First, Clipstart adds a reference to the original movies to its database. Then, it starts copying the movies. After each movie is copied, it's reference in the database is updated to reflect the new location.