Where will believers spend eternity? Since Jesus said, "No man goeth into Heaven, but He who hath come from Heaven," John 3:13. Where then is the place that Jesus will prepare for us...that we will be with for eternity?
Disembodied souls now live in heaven or hell.

We are confident, I say, and would prefer to be away from the body and at home with the Lord. (2 Corinthians 5:8, NIV)
Then he said, “Jesus, remember me when you come into your kingdom.”
Jesus answered him, “Truly I tell you, today you will be with me in paradise.” (Luke 23:42-43, NIV)

After the final judgment their will be a new heaven and earth and the disembodied souls in heaven and hell will also receive new bodies. (Rev ch 19 &amp; 20)

However, I admit that I worship the God of our ancestors as a follower of the Way, which they call a sect. I believe everything that is in accordance with the Law and that is written in the Prophets, and I have the same hope in God as these men themselves have, that there will be a resurrection of both the righteous and the wicked. (Acts 24:14-15, NIV)

The verse you mention is a different subject all together. Jesus was trying to explain spiritual things that could partly be comprehended by similar earthly things. However the deep things Jesus had to say about his being sent from heaven to the world to die and resurrect for the salvation of all men who believe does not have earthly references to refer to. In fact this deep knowledge of salvation can never be arrived at by a human ascending into heaven, into  the region of absolute and eternal truth, so as to look upon it face to face. No man has ever done so.  The only way this knowledge can be attainted is by the One who came from heaven. He alone through the incarnation is the one that descends and rises back into that eternal place who alone  possesses that knowledge and declare it to men. By faith in Him and his death, we also rise to live with him, first the soul and then the body. Upon faith in this eternal son the descended and ascended back into heaven does one obtain life and knowledge.  This was too much for Nicodemus to understand at the time as we was stumbling over smaller things such as the new birth which have its fruits seen here on earth and referenced to earthly things to help us understand it.

“You are Israel’s teacher,” said Jesus, “and do you not understand these things? Very truly I tell you, we speak of what we know, and we testify to what we have seen, but still you people do not accept our testimony. I have spoken to you of earthly things and you do not believe; how then will you believe if I speak of heavenly things? No one has ever gone into heaven except the one who came from heaven —the Son of Man. Just as Moses lifted up the snake in the wilderness, so the Son of Man must be lifted up. (John 3:10-14, NIV)