Let's begin by examining the two texts to which you refer.
Now the earth was formless and empty, darkness was over the surface of the deep, and the Spirit of God was hovering over the waters.It's important to note that the Bible deals with two types of darkness and two types of light. The first types of light and darkness are spiritual and the second types are natural.
And God said, "Let there be light," and there was light. God saw that the light was good, and he separated the light from the darkness. God called the light "day," and the darkness he called "night." And there was evening, and there was morning, the first day.
(Gen. 1:2-5 NIV)
God made two great lights, the greater light to govern the day and the lesser light to govern the night. He also made the stars. God set them in the expanse of the sky to give light on the earth, to govern the day and the night, and to separate light from darkness. And God saw that it was good. And there was evening, and there was morning, the fourth day.
(Gen. 1:16-19 NIV)
On the first day God commanded spiritual light to go forth into the earth which had been devastated by the fall of Satan. Before Satan's fall there was only spiritual light, but after his fall spiritual darkness covered the earth.
From reading Second Corinthians 2:1-6, we have further confirmation that it was spiritual light that God spoke forth on the first day. These verses compare what God had done on the first day with spiritual light coming into our hearts when we receive the Gospel.
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