No, Kindle collections are more like tags than folders. You can have books in more than one collection, but they do not nest (though I wish they did).
You can tell the plugin to sort your collections alphabetically, but as you read they will unsort (if you're sorting by collection on the Kindle). If you sort by title on the Kindle, the collections will stay in alpha order but sort in among your books. This leaves two options. Sort alphabetically on the Kindle and use a prefix that will put the collections at the top, or sort by collections on the Kindle and re-do the collections regularly to put them back in order.