Amplitube 4 & Rig Kontrol 3

I don't have the Kontrol pedal, but according to Sound On Sound, the VST instructions are embedded in the audio.  As such, they're probably proprietary and not compatible with Amplitube.
 
The best you could likely do is use it as an audio interface.
 
*I could be wrong, my hypothesis is just from owning Amplitube and Guitar Rig, and from reading one article.  

I figured it out.  I had to select Rig Kontrol as a MIDI input in Cakewalk Sonar settings, I guess it just works as a USB device with Guitar Rig.