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Aside from using it for conversion -- for which, as several wise people have said, the best thing to do is just use the command-line tools to do batch conversion -- calibre is really outstanding for organizing your library.
The critical thing to remember is that calibre organizes books, not files.
The way you are doing it (and most of us did, pre-calibre) is using the filesystem to store metadata -- a very limited and restricted amount of metadata. But with calibre, instead of keeping your metadata in the filesystem (that is, putting your books in folders corresponding to your organizational system) you keep the metadata within calibre. So if, for example, you have a book of short fiction by several different authors, you don't have to worry about whether you filed it under Asmiov or Zelazny; calibre would find it with either one. If you have a book about ancient architecture that compares Egypt, Greece, and Rome, you might tag it "ancient world", "architecture", "Egypt", "Greece", and "Rome", and you wouldn't have to remember that you've got a book in your "Rome" folder that actually has stuff about Egypt and Greece in it too. With calibre, if I wanted to, let's say, pull up a list of all my alternate-history science fiction written by authors other than Harry Turtledove, I could do so with a few keystrokes (or clicks).
Incidentally, a "book" in calibre may be several different files, each in a different format. For instance, I have some O'Reilly pocket refs in both epub and pdf. I use the epubs on my 505, the pdfs on my desktop. Calibre treats both of them as the same book, and just delivers it in the proper format depending on device.
If all you need to do is convert files, the command line is probably the way to go. But try calibre for organizing your books. Forget that its private set of folders exists at all; if you need to get something out of them, export it. You might find that you like not having to remember things like which books are filed under the names of other authors.
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