On my Kindle, I do mix everything, and put either type of books in one or more collections....either Amazon or sideloaded, it doesn't matter (on the Kindle). I'll think about moving my Amazon Kindle bought books into Calibre.....do I do this manually?...I assume there is no sync in Calibre.
Or, like you said I'll do it manually on the Kindle, but this kind of defeats the nice/full features of the plugin?...right?
AND, thanks for the continued help/responses.....