As you are beginning to realize, the Egyptian approach to creation and the ongoing universe differed from the canonical establishment of a single, state religion and philosophy common to all other ancient societies. The Egyptian miracle arose because they refused to limit their vision of creation, they resisted any restriction upon their inner explorations and resultant explanations. For Egypt, there could be no single pantheon of gods, no single cannon of religious beliefs, no unitary creation story, for Egypt perceived the true immensity of creation and found a method to interact which produced a dynamic society lasting for nearly four thousand years.
Therefore, the concepts taught within the Egyptian mystery schools are invariably approached from a multidimensional or multi-metaphoric perspective. It is important for the modern seeker to remember this fact and not limit himself or herself to trying to stick to a single viewpoint. With practice, you will find that your conscious mind actually prefers the inner feelings and knowledge arising from expansivity and communication with the intuitive mind to the more mundane process of conscious analysis. Try it, you will see.
Generally, the Primeval Waters are perceived as very different from visible creation. For example, the Primeval Waters are perceived as undifferentiated substance which is infinite, dark and motionless. The Waters are unconscious, pre-personal and chaotic, containing limitless possibilities for expression of visible universes without restrictions of space nor time. The visible universe is discrete, manifesting in a multitude of forms. The visible universe is full of light and is always in motion. It is structured and functions in an orderly and understandable manner. The visible universe arose from a conscious act of an eternal Creator who arises out of nonexistence and self-creates himself from within the Waters. The visible universe is limited in extent, having a birth and an eventual end.
While the basic concepts of creation did not change over the supremacy of Ancient Egypt, the various stories underwent syncretism, integration and re-synthesis. The creation mythologies of the late old kingdom, middle kingdom and new kingdom grew in sophistication.
For example, the most mystical and sophisticated of the old kingdom creation stories is now known as the Memphite Theology. This formulation of the creator arose from the hand of the mystery school eventually responsible for the formation of the first mesoteric-esoteric school on the earth. A copy of this doctrine was recovered on a stele dating from the reign of Shabako in 700 BCE. This theology dates back to the old kingdom. In this theology, the gods of Heliopolis and Hermopolis are accepted, but they are subordinated to the patron deity of Memphis, Ptah.
First, at the beginning of all else, there is the original creator spirit, ‘Ptah who is upon the great place’. Then follows Ptah-Niu as the Primeval Waters and father of Atum, Ptah-Naunet, the female counterpart of the spirit of the Abyss who gave birth to Atum. This is followed by ‘Ptah the great one’, who is the heart (mind) and tongue of the Divine Company. Rather than the utilizing the anthropocentric representations, Shu and Tefnet, the Creator brings forth ‘heart’ (which was for the Egyptians, the seat of consciousness) and ‘tongue’, the organ of speech. The theology brought into existence a total of eight primitive forms of gods and coalesced all the major creation myths under the aegis of Ptah.
An excerpt from this theology goes,
“In the form of Atum there came into being heart and there came into being tongue. But the supreme god is Ptah, who endowed all the gods and their Ka’s through his heart which appeared in the form of Horus and through his tongue which appeared in the form of Thoth, both of which are forms of Ptah.”
The new ingredient included in the Memphite Theology is the concept of a pervading spirit whose creation is brought about by the exercise of mind and will. For example, an excerpt goes,
“Now heart and tongue have power over all limbs, because the former is to be found in everybody and the latter are to be found in every mouth–in all gods, all men, all animals, all worms–in all that lives. The heart thinks what it will and the tongue commands what it will.”