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Which program you prefer depends upon what you want to do.
I use Calibre because I love the tags feature for collections. But you can also make collections on the device itself. I use Calibre to manage my books, so it's just easier for me to also use it to add books, etc. Plus, I like that books in a series added via Calibre display in order without me having to add the series number to the actual title of the book.
There should be no problems using the reader Library and Calibre so long as you do NOT use both programs during the same session. So if you use Calibre to add books or whatever, you need to disconnect the device, then reconnect it before using the Reader Library software and vice versa.
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