~m
There are a lot of different CBTs, but yes it boils down to changing your thought from negative to positive. What you have to do is specific to you. The program is a guide to help you achieve this in the right order. Emotions are tied to thoughts and beliefs. Do you have emotions you want to change. Be careful in this aim, emotions are a necessary part of our life. Reducing there effects is a good goal but eliminating them is probably impossible and at best would not be a good idea.
Even the emotion anger which is negative is there to let you know all is not well. Better to feel anger than to panic because you don't know what is bothering you. Anger can be changed to sad and sad to happy with the right thoughts. If not happy at least tolerance.
What about instinct? If you read Attachment Theory, you will see that there is a strong belief that we inherit some of our patterns, basically an instinct to react the way we do and that we build on this. Proponents of this believe it can take three generations to break the cycle completely, in other words so you don't pass the tendency. But you can see then that being the case you can change this too even if it is instinct.
I certainly think there is a thought. This is not automatic like breathing, even though the thought might be repetitious. And with it being a thought you have the potential to change it for the better. Even PTSD is a thought or it would not be there. If you did not think about it, it would not exist. Not to say all you have to do to get rid of it is not to think about it, it is a lot more work than that.
Luckily thought can be negative or positive over the same situation. A matter of conditioning.
Basically control of our thoughts to have control of our actions and reactions. The road to a cure.
Here for you,
Davit.
in the darkness of my understanding. I think I "get it" ... that would be nice. Thanks so much for your insight and clarity. 
