This post is a summary of understanding of my analysis of scriptures, surfing across them at a top-level. I had made a detailed post on understanding of matter domain, in depth earlier. This is my understanding in broader terms.
Divinities represent a design pattern
In my understanding, there is a design pattern in evolution across matter domain and biological/consciousness domain. Several of our vedic divinities just represent the design pattern. This design pattern is probably causing the confusions or the multiplicity in our understanding, as the design pattern straddles multiple domains.
Energy and consciousness are not different. They represent the same fundamental unit of design pattern. Energy is the underlying property of physical Universe. Consciousness is underlying property of biological beings. Of course the biological/consciousness domain evolves on top of the matter domain.
But both are Shiva. Shiva just indicates this design pattern.
Mass and Manas are not different. They represent the same fundamental unit of design pattern. Mass is the visible property of physical universe. Manas is visible property of biological beings. Both are Vishnu, Vishnu just indicates the design pattern here.
A pot arises out of clay by the stirrings of clay (by a potter wheel) or cream arises out of the stirrings of the curd (as Chandoyga Upanishad says), manas arises out of stirrings of consciousness and mass arises out of the stirring of energy. But mass and manas cannot be pin-pointed to a particular place but spread all over a body or being.
Duality of perception and reality
Yet clay is not pot, cream is not curd, Manas is not consciousness, energy is not mass. There are zillions of pots (manas, masses) that arise and submerge out of consciousness or energy. As Shankara says सामुद्रो हि तरङ्गः क्वचन समुद्रो न तारङ्गः - Ocean is indeed the waves; but waves are not the ocean.
It's like what Shankara says, watching a huge city in a small mirror. The huge city of consciousness is being seen through a small mirror of manas or the huge city of energy being seen through a small mirror of 'mass'.
The duality in all these can be seen as the difference between reality and perception . Energy is reality. Mass is perception of energy when a particle with energy interacts with higgs field. Consciousness is reality. Manas is the perception of that consciousness by beings.
This the 'dvayam' or duality of perception and reality being different and advayam of only one reality.
How do we overcome this duality (dvayam) and realize the reality (advayam)..? The short answer is, it is not possible. The 'manas' with which we perceive the Universe by definition is limited mirror of the huge city OR cream of the curd or the pot of the clay.
Though manas reflects the consciousness, mass is made of energy, pot is made of clay, mirror reflects the city, unless they give up the form in which they physically exist, they cannot fully fathom what they are.
Though with our manas, limited by its very definition (and hence always perceptive), we cannot fully fathom the consciousness (the reality), we can try to reach the reality behind our perceptions in some way.
Develop an observer - witness component
The design pattern for the evolution of the Universe is an independent non-interacting observer or witness driving the evolved/evolving. Dark matter driving matter evolution or catalysts driving chemical evolution, enzymes driving biological evolution et al follow the same pattern.
In those lines, developing a 'witness' component in our manas (sAksi) that detaches itself from our own actions and observes Universe, all its matter and beings including our own body and its actions, takes us 'closer' to reality, though we can never reach the 'reality'. This is the 'manas-sAksi'.
But the challenge again is, it is physically impossible for us to develop a totally detached manas-sAksi in us, because finally manas-sAksi is also a part of thoughts in the physical body. But to whatever extent we detach, we see other perspectives too as equivalent to our perspectives.