Paul, in 2 Corinthians 12:2, refers to the third, heaven, which is the abode of God. " I know a man in Christ who fourteen years ago was caught up to the third heaven... "
1st - atmosphere
2nd - outer space
3rd - God's abode
These ancient illiterate shepherds got their divinely-inspired cosmology, physics, geology, and biology right right, they just missed a few decimal places here and there.
The division you referenced is between the waters (fluids, gasses, plasma) above (outside the earth's gravity field) and the waters (fluids, plasma, gasses, and (eventually) dust) below the divide. That which was above became the (remained) as the sun, other planets, moons, asteroids, etc.
That which was below became (is) the earth.
But then the waters below are said to be “gathered into one basin” (one ocean) just as the plate tectonics tells us now - and despite what the ancient Israelis actually saw as separate seas and oceans. The visible sky is, of course, above the seas. You're mixing up a physicist's “fluids” with an old shepherd's “waters” - but both describe accurately the same thing.
Notice that plants created next. But still in the proper sequence.
Because you can't see the stars and moon UNLESS there is a free oxygen and nitrogen atmosphere - which did NOT happen until AFTER the plants created oxygen from the impenetrable and poisonous CO2 clouds at the beginning. (The moon was formed by collision before plant life has been found - though not much before.
Thanks for the ping!