That comment about not knowing what to do, you are taking out of context. What Herman meant, was that they weren't sure what to do with the new quarterback in the way of adjustments. JT did look a little overwhelmed. But boy he came on, didn't he?
Clearly, it was the adjustments made to the defense while JT was growing, that brought about such incredible growth in the team. JT need an experience and coaching, he got that and the results speak for themselves. Anyone the questions Herman's abilities as a quarterback / offense of coordinator, are some of those knee-jerk reaction everybody is now speaking of.
The work of Chris Ash and Luke Fickell to make that defense transform itself, made them the unsung heroes of the championship run.