The thoughts that arise in your mind, have a cause. They are produced BY the mind as a result of thinking. They do not show up out of nowhere. Nor are they generated without intention, because "there are no neutral thoughts."
Ego thoughts are reactions, or effects, in response to a perceived external cause. They happen in a split mind in a state of dissociation. One part of the mind sees itself as causing the other part of the mind, and this produce effects. The effects are thoughts of judgement, reaction, threat and fear. These reactions also produce all the ego emotions.
If you believe there is a cause outside of yourself with the power to do something to you, you will have a "reaction". However you are reacting to your own perception that you are being threatened or caused against your will. The belief in this cause splits off part of the mind and pits it against the rest of you. And you can't believe in being caused without also believing there are effects.
The mind generates both the sense of being causal, and the sense of being affected by that cause. ie that you are "doing this to yourself". In the split mind, ie the ego, this dissociation leads to all reactions.
So for example if you perceive there is an external threat of some kind, or a person having power to affect you, your mind will not only believe in being caused, it will also believe in being affected. Cause and effect alway exist together. Your mind will manufacture what it believes should be the "effects", results or consequences, corresponding to the severity of the threat.
This is also because there is a hierarchy of illusions. If you believe there is a very big threat, you WILL have much bigger reaction. The intensity, size, seriousness, importance or value of the perceived danger, which is a belief in YOUR mind, produce a corresponding effect.
For example there was a time when my wife had cancer, and when this was diagnosed, and through the later surgery, I was stricken with intense fear thoughts. And they would not stop erupting. They were strong and persistent and were in direct response to "how serious" I believed the situation was.
It was interesting though that because of this intensity, I got to see first hand the way the hierarchy of illusions works. The ego, in effect, insists that you SHOULD react with a given amount of severity, based on how severe the cause is. Bigger problems call forth bigger reactions. More serious problems have stronger "temptation" and inspire much larger responses.
So I at least got to see that the only reason I was having such a big fear response, with my mind flooded with terribly fearful thoughts every few seconds, was because of this supposed hierarchy. I didn't HAVE to have such a big reaction, and I shouldn't have been having it based solely on the seriousness of the supposed situation. But there it was. Big perceived threats, produce big reactionary thoughts.
You can see in the course a trend whereby it's asking us to not only transcend the hierarchy, but also to stop being affected by external causes. It's moving us towards a reintegration of the dissociated parts of mind, and to stop attacking yourself. And thereby it's bringing about "peace of mind", calmness and quietness of thought, simply as a result of removing your BELIEF IN the hierarchy of illusions.
It would be denial to say that your mind can be peaceful while still having attack thoughts, while still having ego thoughts, while still being plagued by emotional reactions, or while you're still riddled with fear. There is no peace there. Peace arises from the ABSENCE of ego thoughts, having been placed with God-like thinking, which leads to only loving, peace-inducing experiences.
A mind which does not believe the hierarchy and is not tempted by external causation, does not HAVE these reactions. This is reiterated in the secret of salvation, ie "you would not react AT ALL to figures in a dream that you knew YOU were dreaming." By remembering its a dream and its coming from us, we step out of the "reaction mode". And if you can't react, you can't have reactionary thoughts or emotions. And this leads to the mind becoming quiet and undisturbed.
So really it is your mind that makes the ego thoughts. And it makes them both in the form of attack thoughts, and in the form of reactionary thoughts. Where there is attack there is cause, and where there is cause there is effect. YOU make the thoughts that keep flooding your mind with fear, based on false perceptions. Without false perceptions, you have no basis for CAUSING negative effects because you aren't thinking in an attacking way.
So it's not so much that you have to spend time trying to watch thoughts come and go, or try to ignore them, or deny them, or control them. It's more a matter of needing to heal your beliefs and undo the split in the mind, so that you don't PRODUCE all these attacking thoughts.
What this really points to is that, your mind creates its own suffering, your mind creates all symptoms, your mind creates all reactions, your mind puts in place all bodily states, and you are responsible for healing the split so that you don't MAKE these things in the first place.