Sandy, sometimes it is helpful to check several Bible versions. For example :
The Holman Christian Standard Bible The King James Version (Authorized) "Now the earth was formless and empty, darkness covered the surface of the watery depths, and the Spirit of God was hovering over the surface of the waters. "
The Good News Translation ""the earth was formless and desolate. The raging ocean that covered everything was engulfed in total darkness, and the Spirit of God was moving over the water. "
New Century Version GOD'S WORD "The earth was empty and had no form. Darkness covered the ocean, and God's Spirit was moving over the water. "
God's Word Translation "The earth was formless and empty, and darkness covered the deep water. The Spirit of God was hovering over the water. "
New International Reader's Version "The earth didn't have any shape. And it was empty. Darkness was over the surface of the ocean. At that time, the ocean covered the earth. The Spirit of God was hovering over the waters."
The Hebrew word being translated is teh-home'. It is also found in the KJV @
Gen. 7:11 "In the six hundredth year of Noah's life, in the second month, the seventeenth day of the month, the same day were all the fountains of the great deep broken up, and the windows of heaven were opened.
Gen 8:7 "The fountains also of the deep and the windows of heaven were stopped, and the rain from heaven was restrained;"
So from the above, I would suggest that the deep spoken of is either the "waters above" atmosphere or the "waters below" atmosphere Gen.1:6 and therefore was created as part of the earth.