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That is not a bad way to do things. If your library is getting large then you might want to use 'ondevice:true' in the search field to restict the display to those books that are on the nook and thus reduce the size of the list to scroll.
There is also the option of once the Nook is plugged in of switching to the Device view and following a similar procedure from that view. By its very nature the Device view is restricted to books that are on the Device. I believe that you may also get visibility there of books that were NOT loaded through Calibre which might be useful.
Which technique you prefer is a personal preference - neither way is necessarily the 'right' way.
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