Unconscious is more of a psychoanalytic term, subconscious is used in some other fields, particularly hypnosis and self-help movements. The difference in I believe is the psychoanalytic principle that there is a region of the mind that is inaccessible, whereas some of us could make the argument nothing is inaccessible, but rather available if accessed in the right way. Thus sub meaning beneath. Subconscious isn't used much in academic circles.
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