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in general you connect ports; output ports to input ports; connections are usually drawn as lines between output ports into input ports;

once the jack service is up an running you'll have these system:capture_N ports that represent the physical sound device line-ins or microphone(s); and the system:playback_N ports that are the physical line-outs or speakers, headphones, whatever... in JACK-parlance this is what you really have to know, because no proper device names will ever appear to be seen... iow. you'll need to understand that "system" represents the sound card device in charge.

for qtractor, you connect the output of some other device or application (eg. system:capture_N ports) into qtractor's own input buses ports (eg. Master In); and its own output buses ports (eg. Master Out) to some other device or application inputs (eg. system:playback_N ports).

is it clear now?

hth.
byee