Ah - I have always considered the waters of heaven to be the gas tides, driven by the stars, that created the sun and the planets. In a metaphorical sense it is true - there is a flood of gass and heavier elements.
Sure, it ain’t orthodox, but what you expect from a three religion guy!
Water is ubiquitous throughout the universe and I have read how a lot of water could have accounted for an early cooling and crustal formation at a time when classical models predicted a magma surface.
And now we have evidence that massive amounts of continental crust were produced almost immediately upon Earth formation.http://info.anu.edu.au/ovc/media/Media_Releases/2005/November/181105harrisoncontinents
Stars don't come from nothing. Nor do planets. We can see the slow, steady aggregation of gases into stars. We have pictures, again testifying to the glory of God. Stars form from clouds of hydrogen gas. The heavier elements get spun out and away from the protostar. Eventually, the star's gravitational field gets strong enough to light the star. It is another flare of light, with the sudden solar wind forcing the light gases well out and starting random aggregations of heavier elements spinning and collecting. Getting bigger while orbiting the star. Outer planets catch a lot of the gas blasted away when the star ignites. Inner planets are looking at the heavier stuff that doesn't shift much under light pressure.
You're complicating things. The "firmament" and "water above the firmament" part are basically the ancient people's way of explaining rain. They saw water falling from the sky (firmament) which appears like a blue ceiling and concluded water exists beyond it, which is what rain is, as it "fell through".
Liberal verbal gymnastics can make any creation mythology appear to parallel reality, if you ignore the simple details.