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That the "the Word [the Son] was with (apud, πρὸς) God [the Father]" means that the Father and Son are distinct Divine Persons yet inseparably united (since God is supremely simple/one). St. Thomas Aquinas writes (De veritate, q. 4 a. 2 s.c. 2):
In the Gospel according to St. John (1:1) we read:...