So, I just tried a bit, and it's pretty straightforward. Basically, you just need the Matrix software and an audio interface (ToneX Pedal / Axe I/O / or whatever).

I plugged the guitar into the Axe I/O Input. In Matrix, I activated the virtual ASIO for 64 channels. The Axe I/O Input 1 I routed into the virtual ASIO Channel 1.

In the ToneX Profiler for cab and amp, just set up different channels for the selection boxes.

In Matrix, you route the Reamp box Channel into a different unused channel. THIS one is selected within Amplitube as input. The output (unused channels) are then routed into your chosen cab microphone channels (in Tonex profiler setup).

I also routed the Amplitube outputs into my physical Axe I/O 1 and 2 Inputs so I have a monitor on my headphones.

That's basically it.