I'm still new to Linux audio, but I hope Jack will work better with SDL/PulseAudio better in the future.
For instance, I had to edit two files to get Schism Tracker which is normally SDL, to use PulseAudio while Jack was running.
I added these lines to /etc/asound.conf
## Not mandatory
I also had to add these lines to /etc/pulse/default.pa
load-module module-jack-sink channels=2 channel_map=front-left,front-right
And I installed nearly everything about PulseAudio and Jack through yum on Fedora 14 Updates-Testing. I spent a lot of time searching for a solution, and had to ask about it over at LinuxMusicians.
Code is from http://proaudio.tuxfamily.org/wiki/i...tle=PulseAudio