How can we, in our compromised state, actually sort out and identify in our mind, what thoughts and emotions originate with the higher self versus the deep subconscious?

This is best done by the heart. There is a kind of inner sensing and intelligence conducted with the heart itself to be a kind of truth detector with respect to what is in divine alignment and what might not be. You can think of it as a kind of "love muscle," a love detector that sees the good in things, or bad as the case may be, and will resonate strongly with positive and happy feelings when contemplating something that is divine in essence and carries with it a message of love, a higher truth of some kind. So this is more an intuitive assessment than a cognitive exercise of logic and reason. This is not natural for many who prize their ability to think and reason. It may satisfy the ego to have sharpened one’s faculties in carrying out a verbal argument and defense of one’s beliefs, but whether one’s perspective is in alignment with known facts and information is not the same as knowing it is in divine alignment, which transcends the question of literal accuracy in conforming to an intellectual construct based on beliefs that might be inappropriate if they are based on inadequate information. People live largely in ignorance of many aspects of reality outside their awareness or beyond their understanding—even things they see happening around them but are misinterpreting as to their origins, motives, and meanings. This is the human dilemma in a nutshell, that you are essentially like small children in many ways where you do not have yet your adult understanding, so your thinking will be less deep and comprehensive and there will be many gaps in knowledge still and with a poor understanding of the meaning of reality and its possibilities. This state of ignorance will leave you in a kind of vacuum and not in the best position to make choices and plan your life and carry it out with the greatest and most meaningful experiencing and consequences.