scook
If you are going to place reference tracks in the project, the reference tracks should not go through any of the project processing. The tracks should be routed directly out to the audio interface or to a bus that bypasses the master bus and is directly routed to the the audio interface.

What about room correction software like IK Multimedia's ARC2 VST? I would imagine that both my material and the reference track should go through it.

Yes, Magic AB works fine with Sonar X3.
 
I knew I had wanted to get it, but when I moved up to Sonar X3 and recognized I would want to do some things with a fresh approach I decided to get Magic AB at the same time I moved to X3.  I've been using it and it's great.  I've found it does not take mp4 songs straight from my iTunes music folder, but it takes mp3s fine and I have plenty of those.  I can convert mp4s to mp3s if I need them for reference purposes.
 
As a side note, I also use the Focusrite VRM box, and the combo of having reference tracks easily comparable, and being able to toggle through different speaker types on an A B basis between a song I'm working on in X3 and reference tracks is both pretty neat and pretty convenient.  It's pretty cool.  And Sonar X3 is fantastic!