Eru holding Eä (The universe) in his thoughts/mind
"But since Eru was not bound by the Theme, nor by the Ainulindalë (as made by the Ainur), it would be rash to assert that He is or will be bound by Eä realized; since He is outside Eä but holds the whole of Eä in thought (by which it coheres)." - Nature of Middle-Earth: The Primal Impulse.
"“He [Eru] is outside Eä but holds the whole of Eä in thought (by which it coheres).”" - Nature of Middle-Earth: METAPHYSICAL AND THEOLOGICAL THEMES
Note: This particular extract had this commentary on the matter above. The below text isn't Tolkien's words, but rather an exploration of Catholic thought, aka the doctrine Tolkien followed. His Legendarium was a fundamentally Christian work, with Letter 142 making this clear - "The Lord of the Rings is of course a fundamentally religious and Catholic work; unconsciously so at first, but consciously in the revision."
"In Catholic metaphysics, the existence of the material universe and all that is in it, is contingent: both in the sense that it does not exist by necessity but rather by a gratuitous act of Divine creation, and in the sense that its continued existence, in all its parts down to the most minute particle, and at all moments, is due to God’s continuous (from a temporal view) willing of its existence. Its Catholic formulation (as so much else of Catholic metaphysics) is due to St. Thomas Aquinas, who greatly elaborated and expanded upon the contingency of existence. Tolkien’s particular statement here, that the whole of material and temporal existence (Eä, “the World that Is”) “coheres” (< Latin co-haerere, literally ‘stick together’) in Eru’s thought, also clearly echoes Scripture, in particular Col. 1:17: “He [Christ] is before all things, and in Him all things hold together”. The ongoing contingency of existence is also reflected in Acts 17:28, where St. Paul, quoting (ultimately) Epimenides (who however had Zeus in mind), says to the gathered Athenians: “For ‘In him we live and move and have our being,’ as even some of your poets have said”."
"And at last the Vision was renewed, but it was not now remote, for he was himself within it, and yet he saw that all was upheld by the hand of Ilúvatar..." - The Silmarillion: OF AULË AND YAVANNA
Note: A reference to Eru sustaining creation.
Note 2: To make it clear, the universe is a 4d structure, with time and space repeatedly being mentioned in reference to it. For instance, the quote below
"...on a brief episode in History, and on a small part of our Middle-earth, surrounded by the glimmer of limitless extensions in time and space." - Letter 328
"The Valar entered into Eä and Time..." - Nature of Middle-Earth: OSANWE-KENTA
"...the Elves would have said, to have passed with free will out of the physical world and time (the circles of the world)" - Nature of Middle-Earth: NOTES ON ÓRË
"When Eru gave being to this design, in general and particular, and it became Eä, unfolding in Time, He set in motion life and growth, or those processes which would in time lead to this. But when he permitted the Valar to descend into Time, to carry out in Eä (or reality)..." - Nature of Middle-Earth: Powers of the Valar
Also, the phrasing "Eä and Time..." does not mean the two are separate. Both the physical world and time are part of the universe, Eä, as seen in both Letter 328, their coupling under the circles of the world (world being universe), etc. This case is purely wording.
Eru exists in a higher state of reality
"...that when the Creator made it real (that is, gave it the secondary reality, subordinate to his own, which we call primary reality, and so in that hierarchy on the same plane with themselves) they desired to enter into it, from the beginning of its 'realization'." - Letter 200
Note: This is consistent with wording which describes the Ainur as entering from a higher reality into the universe, given that they resided with Eru in the beginning
"...the Valar to descend into Time, to carry out in Eä (or reality)" - Nature of Middle-Earth: Powers of the Valar
Eru as author
"No, Frodo 'failed'. It is possible that once the ring was destroyed he had little recollection of the last scene. But one must face the fact: the power of Evil in the world is not finally resistible by incarnate creatures, however 'good'; and the Writer of the Story is not one of us." - Letter 191
"But the One retains all ultimate authority, and (or so it seems as viewed in serial time) reserves the right to intrude the finger of God into the story: that is to produce realities which could not be deduced even from a complete knowledge of the previous past, but which being real become part of the effective past for all subsequent time (a possible definition of a 'miracle')." - Letter 181
"The Valar had no real answer to this monstrous rebellion — for the Children of God were not under their ultimate jurisdiction: they were not allowed to destroy them, or coerce them with any 'divine' display of the powers they held over the physical world. They appealed to God..."
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"So while God (Eru) was a datum of good*" - Letter 156
This is both a simple and a potentially long section, so I'll split that into another post. Hopefully it doesn't come off as a ramble.
To put it plainly, God is Eru, God is writer, God can intrude into the story, but still views it as a story
