I have a "Catalog" Library that I use just to keep track of what I own and i use my own organization on the computer. Once I have all the metadata set up the way in want, I save the books to disk with the organization settings the way I want them, copy the formats column to a custom column for notation purposes, delete the formats (actual books in the calibre library) and copy the empty books to my "Catalog". I don't know if this is more work than you want, but it works well for me. I use Calibre's awesomeness, but keep my (ocd) organization the way I want.
I just typed this up real quick so let me know if it doesn't make sense or needs more clarification.
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