Psalm 104.5-9 describes how God in the beginning created the earth; then how He judged the earth; and finally how He bade the flood to subside—which was the work of the third day: (1) “Who laid the foundations of the earth, that it should not be moved for ever”—this segment of the passage in Psalm 104 refers to God’s original creation. (2) “Thou coveredst it with the deep as with a vesture; the waters stood above the mountains”—this segment of the passage depicts the conditions of the earth which obtained after God had judged the earth, and thus coincides with the phrase “darkness [which] was upon the face of the deep” found in Genesis 1.2. And (3) “At thy rebuke they fled; at the voice of thy thunder they hasted away (the mountains rose, the valleys sank down) unto the place which thou hadst founded for them. Thou hast set a bound that they may not pass over; that they turn not again to cover the earth”—this segment has reference to the work of God performed during the first part of the third day. “Thy rebuke” and “the voice of thy thunder” are phrases which allude to God’s command in Genesis. That the waters are said here to have “fled” and to have “hasted away” show further how “the waters under the heavens [were] gathered together unto one place” at God’s command as recorded in Genesis. The words “the mountains rose, the valleys sank down” in no way imply that this was the beginnings of mountains and valleys since in verse 6 of this Psalm the mountains were already spoken of as existing. These words simply indicate how the mountains which were once covered by waters would now appear after the waters receded. And so “the dry land [did] appear” once again. Reading further in our Psalm 104 passage, we find these words: “Unto the place which thou hadst founded for them. Thou hast set a bound that they may not pass over; that they turn not again to cover the earth.” These words describe in detail how the waters were “gathered together” by God “into one place” so that “the dry land” would “appear.” Thus do we firmly believe that our present world is but what God has restored.

“Thus saith Jehovah that created the heavens, the God that formed the earth and made it, that established it and created it not a waste, that formed it to be inhabited: I am Jehovah; and there is none else” (Is. 45.18). How clear God’s word is. The word “waste” here is “tohu” in Hebrew, which signifies “desolation” or “that which is desolate.” It says here that the earth which God created was not a waste. Why then does Genesis 1.2 state that “the earth was waste”? This may be easily resolved. In the beginning God created the heavens and the earth (Gen. 1.1). At that time, the earth which God had created was not a waste; but later on, in passing through a great catastrophe, the earth did become waste and void. So that all which is mentioned from verse 3 onward does not refer to the original creation but to the restoration of the earth. God created the heavens and the earth in the beginning; but He subsequently used the Six Days to remake the earth habitable. Genesis 1.1 was the original world; Genesis 1.3 onward is our present world; while Genesis 1.2 describes the desolate condition which was the earth’s during the transitional period following its original creation and before our present world. Such an interpretation cannot only be arrived at on the basis of Isaiah 45.18, it can also be supported on the basis of other evidences. The conjunctive word “and” in verse 2 can also be translated as “but”: “In the beginning God created the heavens and the earth, but the earth was waste and void.” G. H. Pember, in his book Earth’s Earliest Ages, wrote that

the “and” according to Hebrew usage—as well as that of most other languages—proves that the first verse is not a compendium of what follows, but a statement of the first event in the record. For if it were a mere summary, the second verse would be the actual commencement of the history, and certainly would not begin with a copulative. A good illustration of this may be found in the fifth chapter of Genesis (Gen. 5.1). There the opening words, “This is the book of the generations of Adam,” are a compendium of the chapter, and, consequently, the next sentence begins without a copulative. We have, therefore, in the second verse of Genesis no first detail of a general statement in the preceding sentence, but the record of an altogether distinct and subsequent event, which did not affect the sidereal [starry] heaven, but only the earth and its immediate surroundings. And what that event was we must now endeavour to discover.

Over a hundred years ago, Dr. Chalmers pointed out that the words “the earth was waste” might equally be translated “the earth became waste.” Dr. I. M. Haldeman, G. H. Pember, and others showed that the Hebrew word for “was” here has been translated “became” in Genesis 19.26: “His wife looked back from behind him, and she became a pillar of salt.” If this same Hebrew word can be translated in 19.26 as “became,” why can it not be translated as “became” in 1.2? Furthermore, the word “became” in 2.7 (“and man became a living soul”) is the same word as is found in Genesis 1.2. So that it is not at all arbitrary for anyone to translate “was” as “became” here: “In the beginning God created the heavens and the earth, [but] the earth became waste and void.” The earth which God created originally was not waste, it only later became waste.

http://www3.telus.net/trbrooks/MysteryofCreation.pdf