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You can add tags in the main list view. Just double-click on a cell in the tags column, or, select 'edit meta information'. If you select a number of books in the list, and then select little arrow right next to the button, you can select edit meta information in bulk.
For those files already on the Reader, you will have to import them from your computer into calibre, tag them and transfer them to your Reader again.
Calibre has its own system of organisation, which you can't change. I've never used the Sony software though, so I can't compare.
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