Day Two - just water; God places the vault of the sky, the firmament, in the midst of the waters such that half are above the vault and half below - these will be seas.
Day Four - God places the sun, moon, and stars within the vault of the sky, able to cross freely without traversing through any of that water set above the firmament.
Flood - God opens gates in the firmament for the waters to descend, then closes those gates when the flood is deep enough. Experiencing the mortal anguish of a world-ful of drowning pagans moves God to leave the water up above, i.e. cause no successive Flood.
I hope that creates a useable picture.