[Responding to the Skeptic's Annotated Bible, Genesis Verse 1:1]

The author of the SAB claims there are two creation accounts in Genesis. This is a 19th century invention. And because there are no 2 creation accounts, there is no contradiction. I.e. the premise is false, therefore the conclusion doesn't follow. For a more in-depth discussion see Genesis contradictions.
For those interested in the history of the book Genesis, it appears that Genesis is far older than originally assumed by the church. It seems quite likely that Moses did not write Genesis, but compiled it from very ancient sources, clay tablets taken from Ur by Abraham or perhaps given to Abraham by Sem, son of Noah. The ancient form and composition of these clay tablets is still visible in our Bible, but the knowledge of its particular features was lost. It was only understood again after archaeologists had dug up the tens of thousands of clay tablets we now have. See for a brief introduction Who Wrote Genesis? Are the Toledoth Colophons? or The Tablet Theory of Genesis Authorship and see also P.J. Wiseman's original article Creation Revealed In Six Days: The evidence of Scripture confirmed by Archaeology.
On who created the heaven and the earth, all three persons on the Godhead were present and active. In the next verse (verse 2) for example we also see that the Spirit of God was present.
On when the universe was created: I personally agree with bishop Ussher's calculation, but it's not important to agree exactly with him. Everyone who reads the Bible without ‘scientific’ preconceptions will come to the conclusion the earth is some 6,000 years old. Isaac Newton calculated a date of about 4000 BC for example. But note that the age of the earth is thought to be much younger than the age of the rest of the universe, see verse 31.
On the Gap Theory: the author of the SAB gives sufficient links that disprove this theory compellingly