Again I use a firestudio so I assume this is the same.
You can use the meters to adjust your input levels with the knobs on the actual firestudio. Then you can use the sliders on the mixer to mix to your preference, it should only affect the mix of the main outs and the headphones, not what you record. If you've set your input values correctly you should be able to pin the sliders in cubase and get the same level as your getting in the software mixer. If your playing something in cubase you should also see the levels on the daw 1 & 2 channels and be able to mix them to your preference. If you have a click track you should be able to set the output to one of those DAW channels and adjust that in your mix. I'm not sure if you can specify the output channel of the cubase built in click/metronome, so you may need a midi track acting as the click.