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@Marie - Wlecome to MobileRead.
Make sure you have a backup of your Calibre library before you delete your source files, but yes it is fine to delete your originals once you have them in Calibre.
As for the Calibre tree, I assume you mean by "mess" you mean you have things like folders named as book titles amongst your authors, multiple variants of an author name etc. To answer your question, yes as you cleanup your library and rename titles/authors in Calibre the folder structure in Calibre will change as it goes. However you shouldn't care what the Calibre directories look like, as is often mentioned on these forums/sticky you shouldn't be poking around in there anyways. Always use the Calibre UI instead.
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