Technically if you look at the original Hebrew it says all of the "eretz" was covered, that is a word that is more properly translated as "land" rather than "earth", as in, the local land. You can believe a global flood if you want but as the geological evidence all indicates a flood on that scale didn't happen, and I don't believe God would deceive us by planting all of that false evidence in His creation, I personally subscribe to the local flood theory.
Consider the meaning of the word 'firmament'. It is a ceiling separating one floor from another. The floor of one apartment, for example, is the ceiling of the apartment below it. So look at the physical evidence. If there was a floor separating the waters from the waters, we should see it. And we do.
We see the continents, the shape of the continents, the way the continents fit together. Science talks about drift, but there is a better explanation. We see the continental shelf under 300 meters of water. We see how the crust drops off abruptly.
So consider this, the ancient seas were no more than 300 meters deep. The sea floor separated the waters above the floor from the waters below the floor. You can call it a firmament. You can call it a crust, a thin crust separating the waters above from the waters below.
The waters below the floor were deep, even miles deep. When the waters from below the floor came to the surface, the entire earth was flooded for a 150 days until the earth's crust could not support the weight of the waters which were now above the crust.
Then the ancient sea floor collapsed under the added weight of the water that had come from below the sea floor. Therefore the ancient sea floor, the crust between the Americas and the continents of Europe/Africa fell into the deep, displacing the waters and creating the North and South Atlantic oceans.
There would have been immediate run off as water fell into the deep once again and dry land appeared.
That's my theory so far. You might also think there was land between the continents, not just a sea, or maybe there was one big continent with seas where the continental shelf is evident.