OK,

   So, I have Reaktor and the Skanner XT instrument.  This instrument has some morph features that don't seem to be automateable. It's just a bank of buttons that morphs from one snapshot to another. I can't find anyway to capture this.

I'm guess Sonar X2 still doesn't offer a way to record the output directly into an audio track live?  OK. Cool. Is there some other way to do this? Can I do it in stand alone mode in Reaktor?  Would or is there a computer recorder capable of recording the output of a stand alone instrument and simply record it's output on the fly?  

Sure you can do an analog loopback - just route the synth output to a spare pair of interface outputs and record the audio coming back in onto a new track

I finally figured out how to do that. I ran a cable from one of my 8 analog outputs to the 2nd channel input. But it took me a while to realize I had de selected all the analog outputs in the preferences because I never used them.  Ha! Well, it looks like I'm using them now.

Thanks! ;)