I keep a separate directory tree for all my ebooks apart from Calibre. It's all organized by author and it's split into two. One tree I call depot and one final. Both are set up the same except Depot holds any books I haven't looked/verified/fixed yet and the Final tree structure holds the finished copies.
In each folder under depot is the original ebook which I then edit to create a properly formatted (to me) file. I build various versions (.html, .lit), keep an easily editable version for future corrections and move them to the final tree folder structure and delete the depot files. Then I take one, usually the .html, and import that into Calibre. I use Calibre to covert that to my book format of choice for my hardware reader, verify it looks good, has its ToC and stuff and delete source file in Calibre so only the reader version is kept.
Of course, in Calibre, all the meta data is added and a good cover picture. While this way duplicates the book once, I still like to keep my library separate from my tool (like I still do with mp3's and iTunes - I'll manage my own filesystem). It's not really that much space for peace of mind.
Then, I keep it all backed up six ways to Sunday.
