How can I set up persistent connections?
Sometimes you want a JACK setup where every time you start a particular application ("client") it gets reconnected to the same ports. JACK by itself doesn't offer this capability, and most clients don't either but there are a number of ways of accomplishing the goal.
The semi-automatic, script-based one is described in another FAQ.
A completely automatic graphical approach is the QJackctl Patchbay, lovingly described by its creator. Please note that the Patchbay is not the same as the QJackctl Connections dialog. There is comment on the Patchbay page that describes the differences in depth.
Finally, there is fully blown session management (still to be documented)