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hi, i'm afraid I can't help much on the bitten fruit platform--I deal with Linux only--but assuming you go to Setup / Settings and check almost everything is on its "(default)" setting, why don't take the chance and hit "Start" and see what happens?

Once JACK starts alright, hopefully, you may launch your applications (Logic and the other waveform analysis thing); configure them to use JACK for audio i/O and then go to the QjackCtl's Graph, where you may well see those applications as boxes (if all's working right, that is).

By then it's a matter to click-and-drag a connection line from an output-port and drop into a desired input-port (or vice-versa). And that's it. Also, if you're referring to the (old) Connections UI you may also get it to show up as an alternative to the (modern) Graph UI: in the right-click menu from the main QjackCtl window, then select Connections... voilá! maybe that looks a bit more familiar to the tuts you've seen out there?

hth.
cheers