IDF,
Sounds to me like the infinitely more simple case of learning to drive (or your very first hours in the air).
The first couple of hours are fine, because you do every simple gesture consciously. Then slowly you ARE learning, and you go from manual to automatic, and pulling away from a traffic light becomes a single manoeuvre, rather than a "brake-clutch-throttle" procedure. And that's when you stall time and again, and that's when you say "oh, (expletive deleted) I'll never learn", until the "automatics" are in place.
And at some point you get over that hump.
I've never started a PT-6.
But I'm sure some of the procedures have to be engrained in your brain enough to recognise an anomaly in what you're doing.
Everybody makes mistakes while learning. It would be strange if you were the exception.
Wishing you the very best of luck.
Christian