I have the 6i6 which must almost be identical other than the 2 extra inputs.. So did you solve this?
I found that the mix control software only involves the monitoring and playback levels.
Pulling an input fader down does not change the input level to Sonar.
There is a pre set menu and you should be able to re set it loading one of those.
I have no clue what you mean by the term "direct physical card" ? are you calling the interface a sound card? Sound cards are PCI. Anyhow I hope you got it sorted.