I don't think calibre can sync with Kindle, but I may be wrong.
But you can sort by "Date" in calibre so your newly added books are always at the top.
Personally, I created a custom yes/no column and whenever I send a book over to the Kindle I mark it with a nice check mark. I usually end up emailing books straight from calibre to the Kindle, and can't see in calibre which books are already on the Kindle so I found this to be the easiest way to keep track.
Also, you don't have to send books one at a time, you select several books at once, then click Send to Device.
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