The Cuemix Console only affects what you hear of the physical inputs of the MOTU mark 3 series. It is used for zero-latency input monitoring. Each input and output can be controlled separately, so, theoretically, you could have a separate mix of all the inputs on each output. Cuemix is not dependent on software; in fact, recording software does not even have to be open for it to function. Your last settings are recalled and activated as soon as the computer boots.
The Cuemix Console can not and does not affect the playback channels of the software. So you cannot re-route software playback channels in it just as you cannot interrupt the flow of playback channels with it (accidentally or intentionally).
The software inputs can only be affected slightly by the trim knob- this can be boosted 12dB.
For more information, see page 97 in the Windows manual and page 111 in the Macintosh manual.