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.