First edit /etc/pulse/default.pa, you need to add two lines:
In theory now, a restart of pulseaudio should start using JACK for recording and playback, if jackd is running. However, it tends not to work very well: you might find PA hanging and you have to kill -9 it.
This isn't enough of course, now when you log in again, gnome-session will try to start pulseaudio, but not jackd, so nothing works. It's far from the right way, but I edited /usr/bin/start-pulseaudio-x11 (which is started from a /etc/xdg/autostart/ script), as follows:
amixer -c 0 sset 'Input Source' 'Line'
nohup jackd -d alsa &
/usr/bin/pulseaudio --start "$@"
Note that I have to set the input source by hand: something in desktop start up used to do this for me, but now I'm going through JACK it has to be done by hand.