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Calibre is your friend here. Set it up, then import the books from your various sources and have a unified Calibre output without DRM. I have books from Amazon, Storybundle, Humblebundle, Bundle of Holding, Project Gutenberg, FadedPage, Kobo, and miscellaneous university sources via Adobe.
My current unified ebook reader is an Icarus (Android) because frankly the hoops you have to jump through to import into iBooks is a hassle too far. In terms of a unified library management tool, I log everything in LibraryThing - print and electronic, including all my RPGs.
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