Bottom 儿 is the human-legs radical and the entry's filing point. With the head-marker above, the character pictures a person seen head-first, which is exactly the etymology behind 元 first, head, principal, yuan currency.
Top 二 sits above the person below as a head-and-shoulder cap. In the original 元 pictograph the upper element marked the top of the body — the head — so this cap stroke is what gives 元 its meanings head, origin, first, primary.
