The QJackCtl project web page (http://qjackctl.sourceforge.net/
) says this about the server suffix, though unfortunately I don't find it especially illuminating:
A new so called "Server Suffix" parameter option appears to rescue on the situations where QjackCtl falls short on extra, exquisite and/or esoteric command line options eg. (net)jack1/2 differences.
If you know what that means, do tell.
The start up script is a place to put in additional commands to run when Jack starts. I recommend everyone do this:
/usr/bin/a2jmidid -e & #start a2jmidid to create connections between Alsa and Jack midi
I also have other stuff related to setting up particular hardware I have, depending on what I've plugged in at the time.