Lilflyboy,
One would assume/ hope that they would be docked to keep them both charged and securely in place! Agreed the paper backup would probably have to be there on the flightdeck at least during initial phase in anyway.
I also read the original article and I noted that every pilot will be issued with their own iPad rather than a set per aircraft. Good call I say, I wouldn't object to being issued with my own personal iPad!