before the beginning/creation there was three things that existed: 1: god, 2: Spirit, 3: the waters
then the logos, christ, created everything through itself? the logos was created in the beginning; when God spoke?
but the logos did not create that which was before it, or without it?
There are five distinct Jesuses in the NT, with three distinct backgrounds. Only two of the five created the universe, the Jesus of Paul:
1 Corinthian 8:6 yet for us there is one God, the Father, from whom are all things and for whom we exist, and one Lord, Jesus Christ, through whom are all things and through whom we exist.
and, as you say, the Jesus of the author of John:
John 1:2 He was in the beginning with God; 3 all things were made through him, and without him was not anything made that was made.
These both reflect gnosticism, since they're also the only two Jesuses that pre-existed in Heaven with God and were sent from there to earth as God's emissary. These qualities identify their Jesuses with the gnostic demiurge, who had to be the creator because God, being absolutely pure spirit and very remote, would never create the (non-spiritual, implicitly less than pure) material universe. Having created it, the demiurge then mediates between that universe and God.
So when you say above that the waters pre-existed the creation, if that's correct ─ I'm inclined to think the waters are covered by Genesis 1.1 ─ then it's nonetheless not correct for the Jesuses of Paul and of the author of John.