Sometimes to make the idea controversial, atheists depict God as a humanly being residing in the space and then compare him to other fairy tale creatures. To counter this, some sort of logical or may be philosophical answer is needed to the question, "Where is God?" What is an overview of the positions within Christianity about this subject?
While this isn't true for all branches of Christianity, the vast majority of Christianity believes God to be Omnipresent - that is, everywhere at once.
That page lists several verses from Scripture that support this attribute of God.
This generally goes along with the idea that God is Spirit (John 4:24), and not a physical being of flesh and bone. Although some denominations, like the LDS, teach that God is a being of flesh and bone, and that omnipresence has a slightly different meaning.
For many Christians, God is also not limited to our universe. As the self-existing Creator of the universe, He us greater than it, and not limited to the universe.
A number of positions may exist within Christianity, but are they not regarded as contradictory. Most Christians today generally believe that God is omnipresent, throughout the entire universe and beyond.
Daniel 2:28 reflects an earlier belief, telling us specifically that God is in heaven:
Somewhat like Daniel, Acts of the Apostles tells us that God is up in heaven above, seated next to Jesus; a view that has never entirely gone away and is sometimes mentioned to this day:
We then go to the Church Fathers such as Augustine and Thomas Aquinas. John M. Perry says in Exploring the Evolving View of God, page 167, that Augustine taught that God is present in all creatures yet transcends them, but Aquinas said that God is not, and can not be, intimately related to the world.
In the Bible, God the Father is commonly seen in visions as seated on a throne in heaven. This is not necessarily contradictory to the idea that God is omnipresent, since He can be omnipresent and also still take on a form.
Daniel 7 9-14 (KJV)
Revelation 4:2 - 5:6
Obviously, these visions do not depict a God that is of fairy tale quality just because His sits on a throne. They depict a God of unimaginable surpassing glory that even angels shield their faces with their wings.