IIRC, the manual for Stutter Edit also has a walk through on its use in various DAWs (SONAR is included) in the appendices. Pretty much the content of this thread.
 
Regarding the other plugin mentioned above, I would assume the steps should be similar; but when I saw use of a Simple Instrument Track it made me realize that I have never tried to use it in this fashion, and I am not sure if that would truly affect a plugin or not. I have always used these on audio tracks (not synth outputs), using the MIDI input as noted above. Once you bring another MIDI feed into the mix, you may very well need another controller, or to use the plugin in iterative steps.

The Stutter Edit manual has not been updated in years. The instructions for SONAR work but describe a method more appropriate for X2 and older. The method described in msgs #3 & 4 work for X3 and newer. The process is the same for any effect plug-in that reads MIDI data. In summary, the steps are:
1) add the plug-in to the FX rack of the track/bus to be affected
2) Use the VST2/3 drop down above the plug-in UI to "Enable MIDI Input"
3) Add a MIDI track with input set to the controller, output set to the plug-in, enable input echo
 

It worked for me and Finger too. Thanks guys.