This question actually comes from a Facebook group called “Ask an Apologist.”
Diana writes: “The Bible talks about 3 heavens. Most people believe the first layer is the actual sky, the second is the entryway into the ‘real’ heaven and the third is the actual heaven. From a biblical standpoint how do you defend heaven's existence? How do you distinguish the 3 ‘layers’ or don't you?”
I'll answer the second one first, and then move from there. We realize, intuitively, that words have what is called a "semantic range." This means that a single word does not have, at least usually, only one possible meaning. Take the sentence pair: "I love my wife" and "I love pizza." I really hope that the one who utters this pair is using "love" in at least a slightly different way! At least most people do use words in different ways, and the same thing goes for other languages, including Hebrew and Greek. "Heavens," in Genesis 1-2, refers at one point to the stars, galaxies, and universe, and at another, to the sky itself (our atmosphere). How can we tell the difference? The same way we tell in ordinary language: context and intention. We know that when someone says, "I love my wife," they typically mean a relationship-like marital love, not a preference that indicates a passing pleasure, like on the level of pizza. Similarly, we know that Genesis 1:1 posits God as the creator of all that there is, and we have other biblical resources to back this up (John 1, the book of Colossians, Hebrews 1, etc.). So if the context in Genesis 1:1 is everything, then "heavens" will refer to the universe. Later on, however, the perspective clearly changes to the earth itself: things are being created on the earth, and the earth is moving from formless (v. 2) to formed (the rest of the chapter), so that when it talks about "heavens" in any translations in chapters 1 and 2, it's going to be with respect to the sky (we can also see this if we recognize that birds are flying in heaven probably won’t refer to space).
Now, as to how to defend the existence of heaven, I think first we ought to have a good theology of our eternal state. Regardless of one's own eschatology, orthodox Christians tend to believe that to be "absent from the body is to be present with the Lord." So, if one dies, he goes to Heaven. However, once Christ returns, the ultimate state of everything is going to be a New Heaven and New Earth, where the entire universe is going to be "re-vamped" as it were, so that heaven (understood as the place you will go if you were to die right now) is not your eternal destiny—the New Earth is. This is all in Revelation and in the broad picture is uncontroversial (though obviously many good Christians differ on the details).
So, we know that when we die, we will be with the Lord from Paul. We know that, from John 14:6, Jesus is returning to his Father to prepare a place for us (metaphorically speaking--it's not like Jesus is the Greatest Conceivable Construction Worker), so that when he returns or if we go to him we may have it. He frames this place as his "Father's House," and we know from Hebrews 1 that Jesus is now with God "at the right hand." We define heaven as the abode of God, based on Psalm 115:3, Job 1, etc. Therefore, we can conclude with some safety, biblically, that God is in Heaven, and when you die, you go to be with God, in the spiritual (not physical) place of Heaven. I hope that helps a little!