The system assumes that you have both cylinders adjusted fairly close with a SERT. (or they will provide a base sert map to go with it).
Then it uses (on my 2002 model) an o2 sensor in the rear pipe to adjust based on feedback and an ideal fuel table built into the proTuner. I think the newer bikes may use both O2 sensors. I can say that it really worked well on my 2002 motor. It takes a 100-200 miles to dial itself in just right and still keeps adjusting as conditions require to maintain the AFR. The motor has never run better. I can say it ran better than any of the dyno tunes I had done on that bike after it dialed itself in.
Now the "I don't like about it" part;
You cannot get into the proTuner to change the AFR tables it is aiming for.
You can't get any feedback to see what changes it has made.
On the 2002 bike it only gets input from the rear O2 sensor and adjusts both cylinder AFRs based on that feedback.
Summary:
If you want a tuner that just monitors and adjusts AFR for you, and don't care to know what it is doing, then the proTuner is an excellent device based on my results with it...
jb