Now we need to clarify the definition of a "soul". The Biblical definition of a soul is simply a breathing body.
Genesis 2:7 "And the LORD God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul."
Notice that the text does not say that man was given a soul, but rather that he became a soul, when God breathed His breath of life into the clay model formed in His image it became a living soul. And when we have this breath of life we become souls, or people - we have life. We see that Souls have blood...
Jeremiah 2:34 "Also in thy skirts is found the blood of the souls of the poor innocents: I have not found it by secret search, but upon all these."
Not only are people souls, but so are fish and animals:
Revelation 16:3 "And the second angel poured out his vial upon the sea; and it became as the blood of a dead man: and every living soul died in the sea."
So the soul is the life of the body - without the soul, the life, we return to dust, we die, we no longer have a character, we are no longer a person. There are lots of Bible texts that confirm this. Our soul is who we are, our character. And our Spirit is the breath of God that gives us life.
Here in Job it explains it clearly...
Job 33:4 "The spirit of God hath made me, and the breath of the Almighty hath given me life."
So here Job parallels the very words of God that we have already read in Genesis 1:
Genesis 1:2 "And the earth was without form, and void; and darkness was upon the face of the deep. And the Spirit of God moved upon the face of the waters."
Now we have identified that that soul, the spirit, is not a separate person, it is our character, the breath of life from God. We are but a lump of clay, God breaths into us His Sprit and we become a person, a living soul. So putting all these things together we can see that at creation we have…God and His Son creating the world and the creatures in it.
It's just the two of them, it's not a third person moving over the waters, but the Spirit of God, the breath of God, the person of God Himself working through His Son to create.
The stories of the Bible are there for us to learn from, they are examples, God showing us how to live by His word and showing us the great plan of salvation, the great sacrifice that God and His Son made on our behalf. God wants us to know Him and to know His dear Son.