Can you please take another stab at explaining what you are trying to end up with?
It sounds like you have a pre-amp boosting your guitar signal, passing through a mixer, and then into your sound card to get it into Sonar. So far, so good.
But the rest is a bit murky.
Whatever amp sim you are using is most likely an audio effect, applied to the track that is picking up the guitar signal. That being the case, Sonar will record only the clean signal coming in, and then the amp sim is applied as an audio effect, just like any other. The advantage of this is that you can tweak your amp sim to your heart's content without having to re-record the guitar this way.
If you are hearing too much of the clean guitar sound, it sounds like you need to adjust the amp sim effect to be 'wetter' - more of the processed sound.
Or, perhaps tweaking the effect or picking a different preset on the amp sim.
If I have misunderstood your original post, please explain it again and I will try to better assist you.
Bob Bone