Part two of my first post (I got distracted while editing.
):
The structure of the ebooks prior to adding doesn't really matter. The metadata should be getting pulled from the embedded metadata fields, but if you have to rely on the filename, the full path won't get used anyway. There are utilities for bulk renaming files, which could consolidate hierarchical folder metadata into the filename, I believe. (If you need it.)
Once in calibre, you have absolutely no control over the folder structure (see Worldwalker's
informative post on the matter.
)
You can, however add tags as well as arbitrary custom metadata types (for example, "genre" is popular).
Under Preferences ==> Interface ==> Look & Feel ==> Tag Browser (tab) you can set "Categories with hierarchical items" which will show as trees based on the period separator.
You can export books from calibre using metadata templates (see Preferences ==> Import/Export ==> Saving books to disk) including various transforming functions, allowing you to save books outside of calibre's black box library. You have tremendous flexibility, and all you need to do is update the metadata associated with various book records.