Everything in the Torah is rooted in the first Portion of the Week.
Before we were told in Genesis that anything specific was being created, darkness and water were already there. Darkness was to go to the night (Genesis 1:5), when the moon rules, whom Jews use for orientation in time – Jews who not only must be good but also holy. And water can purify. Darkness and water have a special capacity for supporting holiness. The creation of the Universe was fit for holiness from the very start.
(Genesis 1:3) And then G^d said: “May light be,” and light was being.
(Genesis 1:4) And G^d was seeing that the light was good; and G^d was separating between the light and the darkness. This separation was not between light and darkness as a matter of place (that happened already by creating them as separate entities) as will be the case in the separation in Genesis 1:7. This here was a separation in time, as we will see in the next verse.
(Genesis 1:5) And G^d was calling to the light “Day,” and to the darkness He called “Night.” And it was becoming dusk [and the darkness took its place] and it was becoming dawn [and the light took its place], [together completing] one day.
It must be understood as such, because from dusk to dawn, or from evening to morning, is not a full day, but rather only one night. All goes after its beginning.
It does not say “the first day” to stress the dramatic event of the first day. Also, something is only a first if we know that a second will follow. And a second one will make the first one less special. First let it sink in: a day!
G^d had to keep calling the light to go to the day (the verb is in the past continuous tense) and tell it that it was good, while one call to the darkness to go to the night sufficed (the verb is in the past tense), because fittingly holy means: separated for a higher purpose. Also, G^d did not want to fix darkness too much onto the night as it needed to go into the day during the Plague of Darkness.
(Genesis 1:6) And then G^d was saying: “May a firmament become inside the water and may it divide between water and water.” The Rabbis tell us that this became a cause of strife, as the waters below wanted to be above too, closer to the Throne of Glory. I have another idea.
The waters that were pushed up wanted to be below, because they didn’t want almost all of Creation to die in the great Flood caused by them. Then G^d reassured them that the Flood would also be caused by waters from the deep, and that the waters below later would need to drown the evil perusing Egyptians as the split sea closed. Further He explained that the waters below would be so dangerous to cross that Jews would have to thank G^d for any safely completed sea journey; while people around the world would pray for beneficial rain and dew, year round. Precipitation is a sign of Divine generosity as it comers down both for the good and the wicked. In the end of the day, however, both a body of sea water and one of rain water can purify. That is how the water above and the water below became reconciled to their roles.