I think it depends on the interface being used. As an example, one of my motu pieces has 24 inputs. They can either be used as 1-24 alternately labeled in the Track Input drop-down list as 1-Left,1-Right,3-Left,3-Right, 5-Left,5-Right,etc. or 1-Stereo,3-Stereo,5-Stereo. All I need to do is select the stereo version of the channel pair where I have my Synth plugged. So if my synth is plugged into 7 for Left and 8 for Right, I'd choose the drop-down for 7-Stereo.
May sound a bit confusing, but you can see all of your inputs in the Edit->Preferences->Audio->Devices. In my preferences. In the box labeled "Input Drivers" should show all of the input ports that Sonar sees for your audio card.
If you need more help, maybe you could post your sound card type and the names of the ports listed in the "Input Drivers" section.
Hope that helps.