Well, like the curate's egg.
2) Worked fine. I could add books to the Calibre library, and view them from the device both ways.
1) I told it to delete a book from the device, and it appeared to do so. It is certainly no longer showing up when Calibre views books in the main memory of the device. However, when I go to the device itself, it is still showing and readable in Mantano Reader.
I wonder whether this is because of the way I added books to the Nexus in the first place? Given that I could not get Calibre to connect with the Nexus, I just copied the books from my Calibre library into a directory owned by Mantano Reader (using the USB cable). Could Calibre remove a book from that directory?
If I had the courage, I would remove all books from the Nexus and start all over again, but at the moment I am too scared to try!