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(what was really the question? :)

I guess you want to setup a patchbay definition in a way that all your pieces (client applications) come together when the so-called studio script is done.

Well, the patchbay profile only deals with restoring client/port connections and you have to get it assembled first, saved to a file (.xml) and then activated on qjackctl, that's right. In fact, that's what the qjackctl -a/--active-patchbay=/path/to/file.xml command line option does: it activates the given patchbay definition file, explicitly.

Side-note: the -a option is the command line way of doing this; you can, however, activate a patchbay profile using the GUI exclusively and that setting (as the command line one as well) will get remembered whenever you run qjackctl in the future. Relax.

The time for you to create and edit that particular patchbay definition file is up to you, just take note that it is all doable while in QjackCtl Patchbay window. There you set the connections rules you want to preserve at all times when the profile is active. It might not sound quite a beginner's thing to do, out of the box, because it hardly is :/ You'll have to setup it at least once, and eventually put it right there in the script as you asked (qjackctl -a option, that's right, remember?).

HTH