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Books sent to the kindle show up as books by default. You can turn that off via the option named "Enable sharing of book content via Facebook etc" in the MOBI Output section of the conversion dialog.
A book will show up as a document on the kindle if it has been marked as a personal doc with the PDOC tag or if it has no asin. Syncing on the kindle works for pdocs or books with a know amazon asin. calibre does not insert known asins into converted books, because converted books are going to be different from the amazon book ocrresponding to that asin. So you will need ot use something like the old mobi metadata editor tool to manually insert the ASIN used for syncing.
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