When it comes to organising collections I have only found one reasonable way to do it, atleast that works for me. I have setup Calibre with a save template that helps keep things reasonably ordered.
{author_sort}/{series_index:0>3s} - {title} - {authors}
That will sort the books into folders on the reader by a folder for the Author, then inside the folder the files will have a 000 - Title - Author format. This works very well if you are adding a series of books at a time as calibre will copy in alphabetical/numeric order, so they are added in the right order for the series.
I'm not sure if that's any help, but it lets me keep things like Discworld in order without losing my mind. Might be able to tinker with it and get it to put an ID infront to order things how you want by default.
Good luck.
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