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I also feel the more tags, the better.
As far as using "different subfolders" goes, you can't make modifications with in the calibre library folder itself. However, you can create additional libraries. First, make a new folder alongside your existing library folder, giving it a unique name. In calibre, click on the icon at the top of the screen that looks like a bunch of books (and tells you how many books are in your library). Then, click on the button for "Create an empty library at new location." To access your new library, click on the little arrowhead to the right of the books icon, then click on the library listed at the bottom of the dropdown menu.
Be careful you don't get carried away adding libraries. There are valid reasons for having multiple libraries, such as two people sharing a computer but each having their own books. I have three libraries, one for books, one for comics, and one for sheet music, since each category requires different custom columns. The ones you suggested should be alright but the more you split up your books, etc. into different libraries, the more places you will have to search to find what you want. Keep in mind that calibre has excellent search capabilities that can be used to find your books, etc. and, if you choose, isolate them into individual lists, all within the same library.
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