Well, Calibre has a horrendous file management system, it saves every book in its own directory on your hard drive. This wastes a lot of space (may not be an issue if you have a smaller collection) and makes the management of these books nearly impossible with a normal file manager.
So if you switch to Calibre, then you have to stick with it, as managing the collection any other way is nearly impossible.
I use the standard Sony Connect software to move the books to the Reader. I only use Calibre if I have to convert something that BookDesigner 5.0 cannot convert.
If you do not want to manage your book files with a normal file manager ever, then Calibre is a good option though.
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