It is not the negative thought that stops you from doing what is best in the long run; it is the failure to counter it. In REBT, we teach people to take responsibility for countering self-defeating attitudes and thoughts. The first step in change is to acknowledge the nonsense you tell yourself without putting yourself down. Then counter the self-defeating permission statement.
Do this regularly, and a good habit is formed. When you stop countering your self-defeating permission statements and excuses, acknowledge this and start countering those permission statements again. Focus on restarting a good habit rather than expecting perfect execution of it.
Self-help is the best form of psychotherapy.