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I have a library of around 1500 books, and I have no problem sorting them on any field using Calibre.
When you add books you have to make sure that the author name is exactly as it is for all other books for the same author, and you also have to make sure that author sort is correctly set. It all works fine for me, no problem.
So I don't have any multiple folders for the same author. I don't have any empty folders either. That is a sign that your library is out of sync with the database. The easiest way to correct that is to delete the entire library and restore from a current backup. You can also move the library to some other folder, and see what is left behind. Save any books.
But I have not yet found a good method to handle series. The best for now is to save a series in a subfolder under the author, and have the title of the book containing an abreviation of the series name and the series index. The subfolder thing Calibre handles, but I have to manually fix the title. Works fine, but it is a little work.
Another way could be to send all books in a series with one save pattern, and after that all books without a series in another save pattern. That way I could write the filenames and folders to reflect [series name and index] without any spurious zeroes and stuff.
This is how I save to device now:
{author_sort[0]}/{author_sort}/{series}/{title} - {authors}
If there is no series, then that part is just left out.
I usually browse my library using folder view.
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