Book Sorter was a particularly handy tool for me since the ebooks I was preparing to import had a mix of author name formats. It would have taken forever to separate them out and identify duplicates.
What I did was point it at a directory filled with folders for each author. I even had duplicates of author folders with different name orders. The folders for each author sometimes contained duplicates with different name orders. I had Book Sorter do a move on the books to a new output directory. The books that got left behind were my duplicates, which made them a manageable subset of the whole collection to deal with.
I did have some problems where some books did not have the author in the filename at all, those typically just had the book title. To resolve that I found "BulkRenameUtility" to be a super help to quickly go in and rename the books that needed it with the author:
http://www.bulkrenameutility.co.uk They have an option to "append folder name" which was a quick and easy way to add the author to the filename.