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The big stumbling block here is expecting calibre to organize its files in a way that is easily accessable to you. Getting over that concept is difficult. The idea is to use calibre to access your books (not files) for you. The biggest mistake I often see people new to calibre make is to designate the folder they are presently using for their books as the one for calibre's library then wail about how calibre messed up their library. Technically, one does not need to keep their original library once calibre has created its library but there is no harm in doing so. I keep my original files just in case I ever want to switch from calibre because I can find the books easily and the file name contains most of the metadata needed (it's also called paranoia). Worldwalker's explanation of treating calibre's folder as an untouchable black box is the best I've seen so far. So far, I haven't been able to find anything easier to use than calibre that can do what calibre does (and I do check out other programs, free or otherwise, from time to time just in case something better pops up). Granted, it does have a bit of of a learning curve since the GUI is a bit strange (at least, it is to me) but there is an exellent calibre forum here at MobileRead that has many knowledgeable users, and often calibre's developer, that will jump in to help a new user out (they have saved my butt many a time).
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