Remember that any "creation" story is simply a myth. It is a made-up explaination of where we all came from. No creation myth is the literal truth or should be viewed as fact.
In addition, there is no universal Wiccan creation story. Any tales like that were written by an individual based solely on their own point of view. I've written one like that myself, but I don't believe that what I've written is fact. Many, if not most, Wiccans that I know of believe in the "Big Bang" theory with its scientific explaination of creation. The stories are just stories.
Where some confusion may come in is that Wiccans believe that the God and Goddess are not only Transcendant (somewhere "out there") but that they are also present throughout their Creation (immanent). But they are present in the physical world as both energetic and spiritual forces, not as physical beings.