ALSA and JACKBefore your start, verify that your ALSA and JACK installation is working. Try to play something with ecasound or alsaplayer, both do support JACK.
alsaplayer -o alsa mysong.ogg
alsaplayer -o jack mysong.ogg
qjackctl is a nice GUI for JACK, highly recommended.
Latency, clicks and dropoutsRead the relevant documentation about optimizing Linux for sound usage, especially on the preemptive patch and the capabilities patch. The whole experience was a lot smoother when i finally applied the patches and recompiled the kernel. there is also the Planet CCRMA project, they develop a Linux distribution tuned for audio stuff, including patched kernels and most of the usual sound apps (though SC3 is not yet in), plus ALSA and JACK.
XI usually run all sound apps as root, taking the ususal security risks like letting an app wipe your whole disk and send flood pings all over your network. and since all jack-enabled apps have to run as the same user as the jack daemon, its all or nothing. if you run anything using X (like opening windows) under root you have to open your X server to connections from root. the
xhostcommand is the key here.
xhost +lets anyone connect to your X server.
A notable exception to the "all as root" rule is the Emacs/sclang combo since all communication is done via OSC. You can run the two (scsynth and sclang/Emacs) on different machines as well, incuding a combination of MacOS X machine and a Linux machine.