Here's the quick setup of Cuemix console:

Enable the master fader (click ON), raise volume.
Choose the output you want to patch TO at the top-right side. Say, analog 1-2.
Enable the input track to use (click ON), raise volume and pan as desired.
Then, route it by pressing 1,2,3, or 4 at the top (1 in this example).

When you close the window, Cuemix will keep the audio routing whenever your computer is booted into Windows.

Cuemix will not interfere with your software's playback or recording.

This functions much like an analog mixer but only deals with the physical inputs of the MOTU.