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.
God is Omnipresent
The attribute of God by which He fills the universe in all its parts and is present everywhere at once. Not a part, but the whole of God is present in every place. This is true of all three members of the Trinity. They are so closely related that where one is the others can be said to be, also.
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:
Daniel 2:28: But there is a God in heaven that revealeth secrets, and maketh known to the king Nebuchadnezzar what shall be in the latter days. Thy dream, and the visions of thy head upon thy bed, are these;
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:
Acts 7:55: But he, being full of the Holy Ghost, looked up stedfastly into heaven, and saw the glory of God, and Jesus standing on the right hand of God,
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)
I beheld till the thrones were cast down, and the Ancient of days did sit, whose garment was white as snow, and the hair of his head like the pure wool: his throne was like the fiery flame, and his wheels as burning fire. A fiery stream issued and came forth from before him: thousand thousands ministered unto him, and ten thousand times ten thousand stood before him: the judgment was set, and the books were opened... I saw in the night visions, and, behold, one like the Son of man came with the clouds of heaven, and came to the Ancient of days, and they brought him near before him. And there was given him dominion, and glory, and a kingdom... (Daniel 7 9-14 KJV)
To him that overcometh will I grant to sit with me in my throne, even as I also overcame, and am set down with my Father in his throne.**
Revelation 4:2 - 5:6
And immediately I was in the spirit: and, behold, a throne was set in heaven, and one sat on the throne. And he that sat was to look upon like a jasper and a sardine stone: and there was a rainbow round about the throne, in sight like unto an emerald... and I beheld, and, lo, in the midst of the throne and of the four beasts, and in the midst of the elders, stood a Lamb as it had been slain, having seven horns and seven eyes, which are the seven Spirits of God sent forth into all the earth.
In the year that king Uzziah died I saw also the Lord sitting upon a throne, high and lifted up, and his train filled the temple. Above it stood the seraphims: each one had six wings; with twain he covered his face, and with twain he covered his feet, and with twain he did fly. And one cried unto another, and said, Holy, holy, holy, is the Lord of hosts: the whole earth is full of his glory.
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.