SOLVED: MIDI Controls for Audio Effects in X3

It should work using ACT.
 
I'm not at mine right now but IIRC correctly press the "Dynamic Mapping" key which should give you ACT control of the current "In focus" FX or Synth. Again if IIRC the C3 button will open the PCR's ACT dialogue so you can see the assigns.
 
They are mapped automatically using the default mappings but changing them to suit yourself is a one time assignment process using "ACT learn". See this video on my youtube page for details on that. Although that is an X1 video it is still relevant for X2/X3 or earlier versions 8.5 etc. - You might want to skip forward to around the 9 minute mark because the first bit is ACT surface setup/MIDI learn etc. which you may have already done. ACT learn starts around 10:40.
 
HTH

Got a response from Izotope:

In order to use MIDI Control in the Harmony module in SONAR and other Cakewalk hosts, you must load the VST version as a Synth. If you do not do this, you will not be able to control the Harmony module from a MIDI track or controller.

SONAR can only send MIDI information to VST plug-ins it classifies as an "Instrument" - so you need to tell SONAR to use Nectar 2 as an "Instrument" before you can use MIDI Control. After taking these steps, you'll be able to find Nectar 2 listed under your "Soft Synths" rather than "Effects," but you'll be able to add it as an insert effect to any track or bus.

Configure Nectar 2 as a "Synth"

1. After installing Nectar 2, go to Cakewalk's Plug-in Manager (Tools | Cakewalk Plug-in Manager).
2. Next, find Nectar 2 in the directory of VST plug-ins that are displayed and select it in the list. (if you don't find it here, you may need to hit Scan VST Plug-ins first.
3. Under the "VST Configuration" controls, press the "Plug-in Properties" button.
4. Make sure the "Configure as Synth" checkbox is selected.

Add Nectar 2 to a Track or Bus

5. Right click on the Effects Bin for the track or bus you want to add harmonies to.
6. Go to the Soft Synths category and select Nectar 2
7. Create a new MIDI track in your SONAR project.
8. On the MIDI track's output dropdown menu, choose Nectar 2 from the list.
9. Playback audio, and use your MIDI Input Device to play and record harmonies.

I have iZotope Stutter Edit and it needs to be set up as an instrument as well (for midi input).  Unfortunately I wasn't able to get the VST3 working in Sonar X3b.  You can go to plugin manager and change it to be an instrument, but when you try to insert it in an effects bin, it only shows up as an effect, and therefore you won't get any midi input capability. The VST2 version works fine.
Jim