I figured it out! Applications like xmms and jack-rack show up in the jack connection list with their PID's appended and this was a bit difficult to reconcile with brutefir, which wants the user to name the in's and out's in a config file. The solution was already built into brutefir and I just configured the qjackctl patchbay to recognize the ports and connect them properly. The brutefir config file should name it's inputs as follows: input 0, 1 { device: "jack" { ports: "", "";}; sample: "AUTO"; channels: 2;};