Remember, calibre manages books, not files. If you import several different formats of the same ebook -- say, tom_sawyer.lit and tom_sawyer.pdf -- they'll both show up as the same book, "Tom Sawyer", and when you select that book, calibre displays which formats you have it in. (if for some reason you didn't import them as the same book, there's a merge function to take care of that) Then, when you're doing your conversions, you select your source format (.lit) and your output format (.mobi) and the new format is added to that book.
The key to success with managing formats with calibre is to remember that the basic unit is the book, not the file. "Book" is an abstraction of files like "file" is an abstraction of tracks and sectors. Manage your books, and let calibre worry about files.