That the Unconscious controls your inner organs is an understatement. It controls everything that is not in your awareness including our habits. Many illnesses develop as a result of Stress you experience by the fight between the Conscious and the Unconscious mind.
Anatomically, the hypothalamus, thalamus, hippocampus and amygdala are parts of the Unconscious. So is the pituitary gland that is responsible for secreting many hormones. It is thus responsible for secreting the chemicals that control so many of the body organs.
If you are chronically stressed, your hypothalamus is constantly stimulated. It causes the pituitary to be active all the time. It secretes hormones to keep the body alert with constricting the blood vessels, raising the heart rate, increasing cholesterol in the blood and also suppressing the immune system. The body is in a fight-flight mode for much longer than necessary. If it is a short-term need the body can handle it. But the problem arises when it is unable to switch off to a relaxed mode.
No amount of argument with the Unconscious mind is going to reverse the process of chronic stress. If the Conscious or the Cognitive mind tries to impress upon the Unconscious mind to change its behaviour, it can do so temporarily. But the Unconscious mind is emotional in nature. It can only be changed long term by working with emotions. Logic has limited effect on it.
However, if you know the process of influencing the Unconscious, you are a winner. Many times you have to decide at the cognitive level how you can influence the Unconscious mind. For example, affirmations are used cognitively to influence the Unconscious. When you repeat an affirmation, it is believed to sink into the Unconscious. It does so only when there is imagery and emotion involved with the affirmations.
On the other hand, the Unconscious affects the Conscious mind too. If you have old unresolved emotional issues, for example, you could behave angrily in many situations without realizing that it is happening. This anger may be coming from some old experience in which you were traumatized. As long as that trauma is still affecting you, the Unconscious mind will continue to make you behave angrily in particular situations. When that anger is expressed fully, then the Unconscious mind perceives the situation as peacefully resolved. It is then able to influence the Conscious mind in having better control over your behaviour,
Most of the ills of society are caused by the angry and fearful Unconscious mind of the people who are considered ill or of criminal minds.
Unconscious mind is positively influenced by meditation. Prisoners who meditate experience less stress. (see link below).
Poor lifestyle decisions are associated with trauma symptoms. These decisions come from our thinking mind. This is an evidence that the Unconscious mind affects the decision making through the Conscious mind. If the decision- making is done with a peaceful Unconscious, it is more positive for everyone involved. When the decisions are made from an Unconscious full of anger and fear, vengeful, cruel and loveless behaviour is seen. This behaviuor is not under the person’s control.
Amygdala is a region in the limbic system that gets stimulated when you get angry. It was once understood that it is able to influence the pre-frontal cortex because the fibres run from it to the pre-frontal region. The pre-frontal region is responsible for decision making. The amygdala when it is active sends rapid fires to the pre-frontal cortex, affecting your thinking. As a result, you can make rash decisions when you are angry. Pre-frontal cortex is not supposed to have fibres running from it to the amygdala. So it is unable to send messages to amygdala and cool it down. Scientists explained that this is the reason, when you are angry, your reason usually does not control your anger.
The Unconscious mind is thus a powerful ally to appreciate and a strong enemy if not given its due respect.
Link for how meditation affects stress in prisoners: