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A. itunes does indeed have a backup copy of all the epub books that you dump into it. to find them use the search function in finder and key in 'epub' in the search field. sort by file type and you will have a list of all the epub books on your mac. restrict the search to the itunes folder and.. voila.. you have a list of all the epub books in itunes.
B. to backup all my books i use timemachine which makes a copy of my entire mac which in turn can easily be restored should i ever require that.
C. i also use kindle, stanza, and goodreader, in addition to ibooks. hence i do have some other epub books spread all over my mac, in addition to the ones in the itunes folder for ibooks. furthermore, i download new books on a regular basis. these quickly add clutter. the best way to organize ebooks in one place, is to download the free program 'calibre'. dump all your books there. it allows you to sift out duplicates, edit and download both covers and metadata, and generally sortify and prettify all your books. you can then choose to download the whole lot to itunes, or stanza, or reformat it for whichever other ebook reader you choose.
QED!
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