Calibre can't automate the process of adding books to collections on the Kindle, but as far as the collections themselves go, they work pretty much the same as the do on the Sony.
By default, if you sort by collections, you'll get them listed in "most recently accessed" order. One useful tip is to prefix all your collections with a character such as "_" (underscore) and then sort books by title. If you do that, you'll see all the collections first, in alphabetical order, followed by the books.
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