Did you follow the instructions on the Jack website about relinking your .asoundrc to use jack rather than alsa handlers?
I think there's also a daemon you can startup with a script using rc.local as well.
Make sure you setup /etc/modules.conf properly also.
Here's what I used as my jack daemon startup:
jackd -R -d alsa -d hw:0,0 -D -r 48000
Use this website if needed for extra info