I don't know if I fully understand your problem, but I'll try anyway.
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Originally Posted by anickson
I have had around 6000 books in my library when I first used Calibre. After several tries, I've got maybe 25,000. I finally figured out that I needed to have two folders, one for my original downloads, one for Calibre to work with. Is there any way to get rid of the duplicate books other than one at a time?
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From what I understand, you downloaded books into Calibres library folder and then added the books to the library, causing them to be copied into the correct library folder, thus resulting in two duplicate files, yes? To disentangle which file belongs to Calibre and which doesn't, you could try letting Calibre move your library to a new position. See Switch/create library in the library button's dropdown menu on the main toolbar. That way, it will only move the files in its library and leave behind the duplicates.
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I started dragging and dropping newly downloaded books from a folder I created for new downloads and it appears that there's only one copy of these files in Calibre. Is that how I'm supposed to get new books added to the library? Can I delete these files once put into Calibre to cut down on the remarkably large files I'm accumulating?
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That's one way of adding books to the library. Another way would be to use the Add books- button in the main toolbar. The way you're doing this now, downloading into an external folder and adding it to the Calibre library via GUI, is the way you're supposed to be doing it. After you've added the books to the library, you can delete the downloaded files, if you wish to. Calibre has made it's own copies that it will use.
Also, while we're on the topic of using Calibre the way it was intended to, don't go manually messing around inside the Calibre library folder. If you want a file from there, ask Calibre nicely via the GUI to give you that file.