@JDriver, if you "import to Aldiko", Aldiko does indeed copy the book into its own folder. If you just "read with Aldiko" the book is not copied, but Aldiko doesn't remember where you are in the book, so if you close the book and/or Aldiko, when you come back in you'll be at the front cover.
And there's no way to tell Aldiko to move its data store or use someone else's data store, and Aldiko has to be the one that puts the book in its data store in the first place.
Very frustrating. Aldiko is a lovely reading experience and I've used Aldiko Premium for years, but it doesn't play nicely with Calibre or Calibre Companion or any external book manager at all.