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There is probably a better way to do this, but what I do with my 350 when in Calibre is go to "Device", and there is a column there (like a tab column) where I can put what collection I want them in. (And remove unwanted collections - the first time I connected the 350 and loaded files to it from Calibre a large number of categories, one for every category i main library view, was created and the books put in multiple collections - drove me nuts!)
I'm not anywhere near my Sony or Calibre, but I'm pretty sure I just right-click and get an "add to library" option that copies the files from the Sony to Calibre library.
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