Since Native American belief systems have pre-contact roots, historical records are not the best of resources to address your question. You might find /r/askanthropology a better venue. More than that, however, I have a hard time understanding the nature of your question: indigenous religious beliefs are an aspect of indigenous culture, whether considering Africa, the Americas or ancient Greece. One can no more explain the origin of traditional religious beliefs than one can explain the origin of other cultural practices. Religions of conversion are another matter, but the origin of indigenous beliefs are beyond explanation the way I understand the term. Perhaps you can clarify.