Putting the books in a particular location and having FBReader scan that location is only useful if you are using books in the FictionBook2 format (.fb2) or OpenReader format (not sure the extension).

Both these formats are open, and they both contain metadata about the book (author, title, category, etc) that allow FBReader to automatically build a library using that data.

I am not positive, but it seems to me FBReader was named because it is a Fiction Book Reader (the FictionBook2 format mentioned above). It does a great job reading lots of other formats too, but I have converted my library into fb2 files specifically for this application.

There are some great tools at http://www.fictionbook.org/index.php/Eng:FictionBook that allow you to convert virtually any book format into fb2 (or other) format. Using Book Designer I converted 122 books, added their metadata, and had FBReader build a library based on Author Name and Category. You can even specify a series for books, and FBReader will put them (ordered) in a sub-category headed with the series name.

It is not a trivial task to convert these books (but at the same time it is by no means challenging, just time consuming) but it saves effort at the other end by just dropping a new book in a folder and having FBReader detect and add it.

And no, I am no way affiliated with the FBReader team (although I filed a few bugs back in my Zaurus days). It is just a great piece of software, and I though I would share my "expertise" in using it. Now, if only ManyBook.net or gutenberg.org would provide downloads in fb2 format I would be a very happy camper.

EDIT: OpenReader format extension is .ePub and manybooks.net does indeed support this format (albeit with a caveat of test, as in "ePub_TEST"). I just tried a download, plunked it in my FBReader directory and, lo and behold, it appears in my FBReader library with the correct author. I don't know if series are incorporated in the manybooks.net metadata, but it is very nice to see an open format download option for these public domain books!