In the end it seemed the simplest way (for me) was to use the automatic adding. I edit the book on my laptop to get all the metadata correct and push it out to a directory on a network share. Calibre running (GUI, minimized) on the server picks it up and files it correctly into the library.
That's what I like about Calibre, it may not always be super simple, but you can generally get the result you want
(Captcha = "book worm", strangely appropriate!)