I'm using Guitar Rig for my guitar sound and often just running the standalone when I'm just playing, but the sounds I create using the standalone does not sound as good in Sonar. Right now I'm trying to get a specific sound I created and when I'm using just Guitar Rig it has a nice distorted sound, but through Sonar it's much "cleaner". Any idea where to tweak to get them to sound the same ?

Normalize the guitar track to 0, and check GR's input level meter; adjust the level if needed. Remember, when you use an amp sim in a DAW, it's always re-amping.

Yeah I was figuring it was a leven thing I just can't figure out where to adjust, but I found out that I can get the same sound be tweaking a bit. In this case the gain on the gratifier. It would be ideal if they were identical, but I can live with it.

Use the gain nob on the track to adjust the input level. You should be able to get identical sounds.