Using Reaktor sequencers inside Sonar - routing?

 OK so here's what you need to do. 
 
You need to add Reaktor as a synth. But even though you're going to be routing MIDI and not audio from Reaktor, you need to point an audio track to it. It's a kind of dumb quirk but unless you do this, Reaktor won't respond to Sonar's transport controls. In other words, Spiral needs to know when you've started playback in Sonar, and it won't know this unless you have an audio track with Reaktor as the input. So on that note, here are the steps:
 
1) Insert Reaktor. In the "Insert Soft Synth Options" dialog, make sure that you have just "First Synth Audio Output" and "Enable MIDI Output" checked. This will insert Reaktor into the synth rack and point an audio track to it. Remember though, this audio track is simply a workaround and you won't actually have any audio coming out of it. 
 
2) Load Spiral into Reaktor. You need to make sure that you have "Toggle Edit Mode" enabled (it's the button directly to the left of the main preset window at the top). This will make the "properties" icon (small checkbox) appear in the left hand sidebar. Click this, and select "connect" from the options below. 
 
3) Now you need to select the MIDI channel on which Spiral will send out MIDI.  Halfway down the sidebar is a section titled "MIDI OUT." Here you can select the MIDI channel you want. For this demonstration, leave it at 1. 
 
4) Now it's time to insert the soft synth that you want Spiral to play. Insert it and make sure "MIDI Source" and "First Synth Audio Output" are selected in the options. Now you have your synth loaded, as well as an audio track to hear it through and a MIDI track through which Spiral's MIDI output will be routed. 
 
5) Set the input of the MIDI track (the IN/OUT buttons at the bottom of the inspector) to Reaktor->MIDI Ch.1 - this will route the MIDI output from Spiral into this MIDI track. 
 
And you're good to go! Hit play and check that Spiral starts playing and that the sound is coming out of your soft synth. If not, check back 

It sounds like you have the other MIDI track's inputs set to "MIDI Omni." Change them to something else, like Ch. 1.