I have also been confused about Christ’s second coming, so you’re not alone! On the one hand, Jesus said to the thief on the cross “today you will be with me in paradise,” (Luke 24:43) but on the other hand Paul talks about those who are dead in Christ being raised when Christ comes again (1 Thess 4:16), the future event we’ve come to call judgment day. Some theorize that your soul goes into a kind of sleep mode until the second coming, so that, for example, the trip to paradise for the thief seemed instantaneous, even though it was not (and Jesus can be excused for what might otherwise be seen as a misleading statement to the thief because God is outside of time). I think the more Biblically sound explanation is that the soul immediately goes to heaven to be with Christ (as Jesus clearly indicates in His story of the rich man and Lazarus – Luke 16:19 and following, especially note v. 22) and then our perfected bodies join our souls at the time of the judgment. In 1 Corinthians 15:35 and following, Paul talks about the perfection of our physical bodies. He seems to indicate that it will be a merging of the physical and the spiritual. In this way, God’s creation comes full circle and becomes fully restored. When God created this physical realm in the first place, He said it was “very good” (Genesis 1:31). It has now been corrupted by sin, and in order for everything to be put right again, God will bring about a perfected physical existence as well as a spiritual one. Accordingly, the Bible also talks about a new heaven and a new earth (Revelation 21:1), in which we, in our physically perfected bodies will enjoy eternal life.
So, to get right to the point… I believe the Bible indicates that the souls of those who have died in faith in Christ are already in heaven in a purely spiritual state, where they, like we, are awaiting the final judgment when a new and perfected and incorruptible physical/spiritual world will be created including bodies that will be similar to the earthly ones we now have, but without any of the imperfections, diseases, genetic malfunctions we carry in our bodies now. And I believe some of the perceived imperfections we have in our bodies – funny looking feet, ears or nose that are too big, knock knees (a trait in my family), etc., will still be present in our perfected bodies, because we won’t have our sin-tainted, self conscious thoughts or the criticism of others to think of God’s perfection as an imperfection any more. Won’t that be nice?