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When I buy a book, I'll disinfect and extract it. I will then pour this book into my own form (one that I can easily transform into PDF, using LaTeX, as I can't stand the epub reader on my BBMini). This is my source copy. It is kept far, far away from Calibre as that will add extra stuff in it that I don't want. I want my source to be clean and untainted by any application (except notepad or equivalent application). This source is in pure HTML (single file), images and CSS.
Using my personal tools, I will then transform my source into epub, mobi and PDF. Those three formats will be entered in my Calibre library. Whenever I update a book (fixing typos), I'll update the source and re-create the three formats again. This will also be noted down in Calibre (by using a version). From Calibre, I'll put my books on my various devices.
My Calibre database is housing on an external HDD which is regularly synced with a copy that is housed in my server (on which my Calibre webserver is running). And I recently added all my epub books to my SkyDrive folder as well, as I recently acquired a Windows Phone.
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