Your using the 6i6 a little bit different than what I would be doing.
I have never had to use Mix control for anything other than setting my buffers and toggling the line/instrument settings.
First the rear 3/4 inputs are for line level so this is where the backing tracks would go.
Because they are line level they are not a problem for 90% of the things you would interface, like a synth, drum machine, DI or even a mike pre amp.
Reason is these devices all have there own level control so this is where you set the input level. There's no need for a second level control and this is standard for most interfaces as far as rear line inputs go.
I have mine set for the input #3 receive signal from my Joe Meek pre amp and the #4 from my Radial Tone Bone acoustic guitar pre amp. I set Sonars record level by adjusting the output levels of those devices.
The #1 input I use for other mikes, like my snare or guitar amp. The #2 is an XLR send from my Bass amp built in DI.
I don't do large sessions any more but I also have the option of using the SPDIF 5/6 inputs via my Yamaha 01V.
If I record my band I use my Tascam which has more inputs.