Same here.  I use onboard card for windows et al, and my interface solely for Sonar and other audio programs. 

One thing I noticed when I had two Asio devices connected (M-Audio Delta LT1010 + Line 6 Guitar Port) was that Sonar chose the Guitar Port to be the device in the "Record Latency Adjustment (samples)" and even trying to change it for the Delta it always returned to Guitar Port.

I use my Mackie Onyx 1220i mixer as my main audio card for Windows and my MOTU Track 16 for Sonar exclusively. I route the main outs of the Track 16 to an input on the Onyx so everything runs through the mixer but the drivers are kept separate. Works very well. I don't let apps take exclusive control.