What is it you get confused about with the 6i6?
It has a few choices for inputs which will show in Sonar as follow ( might look different )
channel 1 left = combi input 1
Channel 1 right = combi input 2
channel 1 Stereo. = when you use both and a stereo source like a keyboard.
channel 3 left rear panel input 3
channel 3 right rear panel input 4
channel 3 stereo rear panel 3/4 together for stereo sources.
Each audio track allows you to select on of those as the input source.
Make sure you open the Mix Control to select if your using a line or instrument.
Normally I never touch mix control for anything other than those toggles and to change the buffer size. Mostly you will only need to mess with it if you use it for fancy multi monitoring set ups.
Otherwise just leave it at the default. I rarely even open it as I have a set up for using all 4 inputs that never changes.
The 5/6 inputs are the SPDIF which I use via a Yamaha 01v digital mixer.
I use output 1/2 for my monitors
Output 3/4 go to a small mixer I use just for headphone mixing.