believing thoughts

In a recent coaching call, the coach said don’t listen to your primitive brain or don’t believe what it has to offer.

How do I do that or how does that work?

The thoughts that my primitive brain offers sometimes seems really true or factual in the moment.

Most of my thoughts create the feeling of defeated, unmotivated, tired, unenergized.

Is that an emotion that I should allow or do I change my thoughts?

My main question is before changing my thoughts about something how do I stop believing my old thoughts that seem true?