[Lady Fitzgerald]

Calibre, if allowed to do its own thing, doesn't organize files, folders, etc. It organizes books. It doesn't care about file or filename size. As long as your OS can handle the filename, so can calibre.

The thing that people have the hardest time understanding about calibre is calibre uses tags to keep track of books and organnizes them within the program instead of in an OS' folder and file hiearchy, which is one reason why calibre copies books from the user's location to its own folder with a simplified file and folder structure.

I feel (and apparently do you) that you are unnecessarily complicating your use of calibre. Unless your PDFs are something radically different from your e-books, such as technical or legal documents, just put them all together into calibre and let calibre do the sorting. If you want to be able to easily see what format each e-book is in (such as epub or PDF), you can create a custom column in Preferences to show that. Then, if you want a listing of only your PDFs, just do a search.

The hardest part people have with letting calibre doing all the sorting, etc., is that calibre uses a simplified file and folder structure of its own store (not organize) ebooks and people who are used to using the traditional file and folder system for organizing have trouble accepting calibre's way of doing it. I personally like to have as much "metadata" in my file names as possible should I ever decide to abandon calibre for another program. Since computer storage space is so cheap nowdays, an easy solution is to keep both your original, klunky, kludgy file/folder system and calibre's own file/folder system and simply ignore calibre's. Worldwalker, one of the power users here, suggests treating calibre's folder system as a black box and never touch it, look at it, or even think about it.

You can get more detailed information about this in the calibre forum.