The mixer level controls that affect cue levels are the Wave/MP3 level control and the Master level control (also called Play control). The terms used will depend on your sound card driver, but basically the 'Wave/MP3' fader controls the level of all sound file types supported by SCS, including WAV, MP3, WMA, OGG and FLAC. The Master level control determines the mixed level of all channels, including the Wave/MP3 control just discussed, as well as CD, MIDI and possibly other controls that SCS is not interested in and doesn't display. Some sound card drivers only show a Master level control, but in these cases this is the equivalent of the Wave/MP3 control.
When you click on the Mixer Levels tab you will see Master Volume and for Wave/MP3 Volume controls for the displayed Mixer. If there is more than one mixer available then you can select a different Mixer from the drop-down list. The level controls and the Save Settings checkboxes apply to each selected Mixer.
For live running (ie for performances) it is recommended that the level controls be set at or near maximum especially if you have an unbalanced connection between your PC and the sound desk. Keeping the level controls high minimizes any AC hum picked up in the unbalanced lead. You can adjust the levels of these two controls using the faders.
To save the current levels so that they will be set each time you start SCS, click the Save these settings checkbox.
There is also a checkbox to Remove saved settings. If you select this checkbox then the saved settings are wiped out, and when you start SCS the current settings of these two mixer level controls are left alone.
You may want to Remove saved settings between productions, when perhaps you have your PC at home rather than at the theatre, but you should Save these settings during a production run so that you can guarantee they are set correctly for each performance.
SCS clears the Mute switch on the Master and Wave/MP3 mixer channels.