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 the position of 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.
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God is outside the Universe in the third heaven Jesus is outside the universe in the third heaven The Holy Spirit dwells within believers
God's power and glory - his presence - fills the universe, the universe answers squarely to him. All non believers are filled with life (breath) that comes from God.
God is aware of everything that is happening, from the biggest events - star explosions etc to the littlest vibration of a subatomic particle.
It says alot about the universe, where is it in relation to God, rather than where we are. But yes, he resides in the third heaven, his presence is here though - hard to describe, essentially he is everywhere at once, he is after all outside of our space-time continuum, and in no way subject to our natural laws - he is after all the creator and ruler of them.
Anyway for reference
1st heaven-sky 2nd heaven - space 3rd heaven - God's domain - what we call Heaven