Docmatix: If you want your books free and organised, buying from iBooks is the worst possible choice. Stick to Amazon and the various ADE-compatible stores (Google, Sony, (most of) Kobo, etc) and you will be fine. There is a small learning curve on how to access your books once you have downloaded them from the relevant stores, and another one on how to free them from DRM (which we cannot advise you on here, it's against forum rules.) None of this is the fault of Calibre programmers.
After that, once you have your books in Calibre, you'll be able to do whatever you want with them, convert formats, edit them, back them up in one place, dump them onto various devices, and so on.
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