A few people have mentioned the Hermetic concept of "The All", and you're touching on that with what you said about the "Atoms" that make up everything, the scientific "Quantum field" that underlies all reality, the singular substance that everything can be dissolved into, where all identity, individuality, time & space just kind of become inapplicable. You're right in thinking that this insight is key to magic and it's application.
You can use all kinds of different words to describe our situation, but really everyone is living in the same universe and trying to explain the same thing, some come to different conclusions and some have more success than others, but everyone is talking about the same Source. I prefer the Hermetic phrasing, calling "The All" the underlying field that everything exists within, "Mind". What you are, your body, mind, and spirit are all manifestations within Mind of The All, all is Mind, there aren't two minds, you're just a little bubble in the infinite ocean, you yourself are intimately tied to this all encompassing mind, your mind and god's mind are one, similar to how Macbeth and Shakespeare's mind are one. How does this play into the application of magic?
Well, your ego, your body, your thoughts, all of them are vibratory fluctuations within the mind of The All, the only thing that makes you a conscious being is something beyond that, your Awareness, this is what Meister Eckhart was talking about when he said "The eye through which I see God is the same eye through which God sees me; my eye and God's eye are one eye, one seeing, one knowing, one love." In Hermeticism this "One eye" is called your Masculine Mind, where your Will resides and sends directives to your ego and mind, sort of like how you can "steer" the directions of your thoughts, but your thoughts sort of produce themselves. Magic comes from the Will, this part of you that isn't controlled by the material will, by emotions, or thoughts, Advita Vedanta calls this entity the Observer.
There's a lot of delusion and fantasy in the esoteric because in reality there have been very few actual magicians and magical orders, for the most part it's lunatics LARPing and occasionally gaining success because they're close but not on the mark. There are a lot of well intending souls who shoot for the stars and hit the moon, becoming "more lucky" than others, but they're still not magicians. There are also many well meaning philanthropic souls who become Buddhist or Theosophical, and rather than enlivening their individuality, they submerge with The All and become living Angels serving its beautiful lovely Will.
Through meditation, you can discover the workings of your mind and your connection to the observer. You can discover the unconscious way you've been using your Will in life and begin to actively use it instead. This is pretty basic self-help stuff, the universe is magical and this counts as magic, but it doesn't make you a Magus. A metaphor for a Magus would be as if Macbeth sat down, recognized Shakespeare, and got into a very profitable alliance, bringing the below to the above, then the above down to the below. This unification, this alliance, is what The Great Work is, in this metaphor Shakespeare would be the Holy Guardian Angel.
I'm not saying you are God, but everything that you are exists within God, at the moment you're just a bundle of habits and passions, vices and virtues, with an empty void watching it all play out helplessly. You have to make the connections here yourself, but through Will, you can unite & subdue your psyche, Soul, and Mind to make that void within you a temple through which the Living God can reside and act through, nothing is lost here either because all of this is still taking place within the same universal mind you are in now, you just become aware of it. Through purification you subdue all your egoic habits that were never truly you to begin with, and make yourself an "Avatar" of the The All to a degree, a truly individual and unique being that is both God and not God. This being would be a Magician, and some people will call me delusional or a LARPer or insane, but with this union of the above and below, you could accomplish anything, the Mind of the All would be to your whim, and truly you would be able to wield the power of Magic.
I hope I've helped in answering your very complex question.