Hi, we’d recommend using Patchbox OS as your starting point ([Beta] Patchbox OS image 2020-11-23) - it has Jack server preconfigured, and also it has amidiauto which by default should handle the MIDI connection between hardware controllers and software programs like Aeolus.
Otherwise, you can use qjackctl or Audacity to configure the Jack backend.
aconnectgui (install by running sudo apt install aconnectgui) is a nice simple GUI for making ALSA MIDI connections - it has always worked better than qjackctl or Audacity for me.
You may also post the output of this command while Aeolus is running:
aconnect -lio
So we can see what MIDI ports are available.