I am also confused about the way calibre treats the ebooks. So I made it simple (for me). I drag'n'drop the ebook from a different folder, so I have the original there (should it happen something to it
). Once the conversion is ready, I delete the copy of the original, to have only the converted book there.
In this moment I know exactly what I edit and how. Well, it has to be one of the formats calibre knows how to edit, but I use only ePub so this is solved.