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What I personally do is use both. I import my books into calibre to convert them and get the metadata right.
I then import them into the sony library (from the calibre folder) to check the appearance of the books, and upload them to my PRS.
Uploading books using the sony software will pre-paginate LRF (BBeB) files so that they open quickly on the reader. This gets much more important for very large books that would otherwise take several minutes to paginate on the reader itself.
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