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Your situation is not unusual and you are not alone. In the terms of this meditation, it is an advanced technique which requires a wealth of self-understanding.
Intentions are the motions, strings of the mind; emotions, of the heart and actions are of the body. When we mix them, the tangle becomes exceptional and control is lost entirely. Seperate and mastery of each individually is the foundation to cultivating their mastery.
In practice:
The greatest insight Gautama Buddha left with regards to your question is the five hindrances. By observing one component (mind, heart, body) without the bias of another influence the effects of the the five hindrances are minimised and you can merge the components with success safely.
Cultivate in harmony
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Buddhist practise is to think in the manner the Buddha taught us to think, such as thoughts of renunciation, good-will and harmlessness.
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Buddha did not talk about the heart and mind. What he taught was the arising of wholesome thoughts and unwholesome thoughts in the mind. The good news for you is that you are aware of this. (Samma Sati or Satipathana) Just continue to practice Satipathana.
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Iβm often in confused stage because my mind says one thing while my heart says something else and my awareness is in total confused mode trying to interpret these two entities.
It'll be difficult to discuss in more details without some concrete examples/instances of the above, for quite oftenly, what one's "heart wants" while one hasn't attained enlightenment ususually is just a romanticized/sanitized way of sayin what one's "desire/lust wants". Just like how many times engaged couples explain away the break-up of their relationship as due to the man/woman simply "following their heart" to cheat on the fiance and had an affair with a different man/woman, etc.