I use pulse-jack from the kxstudio repos and all my non-jack audio issues disappeared.
Simply have qjackctl start pulse-jack after startup or place it in a script with your jackd command. It automatically routes all pulseaudio output through jack. Brilliant.
Same thing for Dream Studio (although I believe KXStudio does it differently, as it’s apparently not multi-user). But, yeah, either pulse-jack solution will take care of this stuff.
Although I don’t set jack to start up automatically in Dream Studio, once I start having to use a JACK app like Ardour, I usually just leave it on afterwards, so JACK can end up running literally for days while we use our main PC as a media center (Flash videos online, banshee music player, etc.)