If the books that you want to add are totally new to calibre (that is, they are not already in the database at all), then just use Add Books and browse to their location.
If the book titles are already in calibre, and the metadata matches up (publisher, isbn, etc), then you can go into the Edit Metada screen and in the upper right portion, Add Format and then browse to the file location.
In either case calibre will copy the file into it's library structure.
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