the PRS600 does not support sorting by folders. adding un-needed folders will only slow the device down.
sorting is accomplished via the collections feature, which sorts by the series and tags sections of meta data. both should be accessible via either sony's reader software, or calibre.
as an example, the Hobbit could be placed within the LOTR series (as book 0) and also tagged with Fantasy, JRR Tolkien, etc. and the reader would have access to the book via all three of those categories. (the same file, it does not make multiple copies.)
the whole thing makes sense really, once you understand how it works.
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