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No sweat. I think you got it almost there. Maybe there's a misconception about what its called a "bus" in Qtractor parlance :) Let me try to explain...

The way to create more inputs/outputs than the default stereo "Master" ones, is in deed by creating more buses, either Input, Output or Duplex. Duplex buses are just a special input and output gang, that you may connect internally via a pass-through feature (cf. the small "thru" button on the respective mixer strip).

Now, take note, that buses in Qtractor are not quite the same concept as in all other DAWs (another misconception: Qtractor is not a DAW; I take it more as an Audio/MIDI sequencer:). I've now realized that this might be one root of many troubled assumptions. Qtractor buses are just a logical aggregation of input and/or output channel ports. That answers your question about the JACK/ALSA connections. Buses are just groups of ports, which are in turn connectible to and from outside applications or devices.

So, to have a multi-channel setup, you must dedicate one bus to each set of inputs/outputs you need. If you have, for instance, a microphone input (mono) and a guitar input (mono) for recording, you'll need two audio input buses with one channel each. Example:

1. Name="Mic", Mode=Input, Channels=1
2. Name="Guitar", Mode=Input, Channels=1

You create new buses in the View/Buses... dialog. Just select an existing bus (eg. "Master"), change its settings and press the "Create" button, simple as that. The new bus(es) should appear immediately on the Mixer
and Connections tool windows.

Following the example above, you then should assign the newly created buses to some audio tracks. Look in the tracks properties dialog (Track/Add Track... or Track/Track Properties...)

Are things a bit clearer to you now? or am I missing the point?

Cheers
--
rncbc aka Rui Nuno Capela