Before the Son was born to Miryam as the man "Yeshua," he was "with...beside...next to" God. He then emptied the privileged of that position and came "from" God when the Ruach "overshadowed" Miryam and he became a human embryo within her.
In other words, before Bethlehem, the Son experienced what was a metaphorical spatial relationship with God. After his resurrection and return to be "with" the Father, he re-assumed his original position before or beside God's throne, even occupying his own throne.
This study goes into greater detail about this:
The Heavenly Council in the Hebrew Bible and New Testament
The Book of Revelation is rich with these royal throneroom images. But this study focuses on those two prepositions in the Gospel of John and 1 John.
The base text is the New American Standard Bible (revised edition 2011). Instead of "Jesus" and "Christ," I have substituted the name "Yeshua" and title "Messiah" to recontextualize the passages into first century settings.
At the end of these lists are definitions of the prepositions, including their cases, from Greek grammar sources.
1:1 — "The Word was with [beside; pros] God"
1:2 — "He was in the beginning with [beside; pros] God"
[In his God's New Covenant translation (1989), Heinz Cassirer renders pros in John 1:1, 2 as: "the Word was by the side of God... It was he who at the very beginning was by the side of God."]
1:14 — "...glory as of the Only One beside [para] the Father"
6:46 — "The One who is from beside [para] God, he has seen the Father"
7:29 — "I am from beside [para] him, and he sent me"
8:38 — "I speak the things that I have seen from beside [para] my Father."
8:40 — "[I am] a man who has told you the truth, which I heard beside [para] God"
[9:16 — "This man is not from [para] God."]
[9:33 — "If this man were not from [para] God, he could do nothing."]
15:15 — "...all things that I have heard beside [para] my Father I have made known to you"
16:27 — "I came forth from beside [para] the Father [or God]"
16:28 — "I came forth from beside [para] the Father, and have come into the world; I am leaving the world again, and going to the Father."
17:5 — "And now, glorify me together with [para] yourself, Father, (with or in) the glory which I ever had beside [para] you before the world was."
17:8 — "...they received [the words that you gave me], and truly understood that I came forth from beside [para] you, and they believed that you sent me."
1 John
1 John 1:2 — "the eternal Life, which was with [beside; pros] the Father...was manifested to us."
- Source: BAGD, 610. Definitions: with: dative it denotes nearness in space at or by (the side of), beside, near, with.
- Source: Dana-Mantey, Manual Grammar, 108. Definitions: Root meaning: beside; by, along.
- Source: Harris, Prepositions & Theology, 171.
with: genitive: from the side of; nearly always denotes a person, and indicates that something proceeds from this person: from (the side of). John 6:46; 7:29.
with: accusative: to the side of
with: dative: at the side of denotes nearness in space, at, by (the side of), beside, near, with. - Source: Thayer, Greek-English Lexicon, 476. Definitions: with genitive: always with the gen. of a person, to denote that a thing proceeds from the side or the vacinity of one, or from one's sphere of power, or from one's wealth or store.
- Source: Wallace, Greek Grammar, 378. Definitions: with genitive the idea is from (the side of) (almost always with a personal object); with dative proximity or nearness.
- Source: BAGD 710-11. Definitions: with accusative: toward. Def. III, 7: by, at, near, be in company with someone; John 1:1.
- Source: Dana-Mantey, Manual Grammar, 110. Definitions: Root meaning: near, facing. with the accusative case: to, towards; beside; against; with, at. John 1:1: "the word was with God."
- Source: Thayer, Greek-English Lexicon, 542. Definitions: with accusative: to, towards; with, with the accusative of a person, after verbs of remaining, dwelling, tarrying, etc.: John 1:1; 1 John 1:2.
- Source: Wallace, Greek Grammar, 380. Definitons: with accusative (almost exclusively). Spatial: toward. Association: with, in company with.
Translation:
New American Standard Bible (updated ed. 2011) (modified)
Sources:
BAGD — Walter Bauer, William F. Arndt, F. Wilbur Gingrich, Frederick Danker. A Greek-English Lexicon of the New Testament and Other Early Christian Literature (2nd ed. Chicago: Univ. of Chicago Press, 1979)
Dana & Mantey — H. E. Dana and Julius R. Mantey. A Manual Grammar of the Greek New Testament (New York: Macmillan Co., orig. 1927; 14th ed. 1957)
Harris — Murray J. Harris, Prepositions and Theology in the Greek New Testament (An Essenial Reference Resource for Exegesis) (Grand Rapids: Zondervan, 2012)
Thayer — Joseph H. Thayer. Greek-English Lexicon of the New Testament (orig. 1889; reprint Grand Rapids: Zondervan, 1967).