There is something even more important to notice about these waters above the firmament. Look again at the passage concerning the second day:

"And God said, Let there be a firmament in the midst of the waters, and let it divide the waters from the waters. And God made the firmament, and divided the waters which were under the firmament from the waters which were above the firmament: AND SO IT WAS. And God called the firmament Heaven. And the evening and the morning were the second day." (Genesis 1:6-8 KJV)

Something is missing there. Do you remember what was said previously? This work on the second day is the ONLY day in the Genesis narrative where the Lord does NOT say it "was good." Therefore, when you consider the statement the Lord makes in Genesis 1:31 where He says that all that was made was "very good"...

"And God saw every thing that he had made, and, behold, it was very good. And the evening and the morning were the sixth day." (Genesis 1:31 KJV)

...it must be considered so in the context of circumstances. The context is the overall work of the preparation of the Earth for Man. The term "very good" does not mean "perfect," and the sea of separation placed between the world above and the world below was not good, but necessary. It would not be until the work of the Lord Jesus Christ on the cross that a way would be made for crossing that barrier (the sea, or waters, above the firmament).