To really grasp the significance of the punishment of death given by God to man for his sin we need to better understand the meaning of the three words. Understanding the body of a man is easy, but what is the difference between the spirit and soul of a man? The author struggled for a long time to understand why the Bible uses both words instead of just using one or the other if they both have the same meaning. However, a deeper study of God's word will shed some light on the subject and hopefully will clear up any confusion for the reader. The reader is encouraged to spend time in God's word doing additional research and then prayerfully meditating on the distinction between the two words. The author believes the confusion comes in that the two words appear to be used interchangeably many times in the Bible (see John 12:27, 1 Corinthians 16:18, Matthew 11:29, James 5:20, 1 Corinthians 5:5, Acts 2:27, Matthew 27:50, Job 7:11, and Luke 1:46-47) and that many people use them interchangeably. But are they really interchangeable? The Greek and Hebrew words for soul and spirit have similar meanings. However, they have different meanings based on the context they are in and are clearly two distinct aspects of man (see Hebrews 4:12 and 1 Thessalonians 5:23). So, it seems obvious there is a reason God uses the two words to describe the make-up of man's being.
There are distinct differences of the two words in the Bible. For instance, the Bible clearly refers to the soul (which we have already learned is the essence of man) as having a destination of either Heaven or Hell (see Job 33:18, Proverbs 23:14, Psalm 16:10, and Matthew 10:28). On the other hand, the spirit is the essence of God given to man (and only man) providing him with the ability to have a relationship with Him (see Job 33:4). This relationship through our spirit manifests itself in the following ways: (1) knowing God (1 Corinthians 2:10-14), (2) serving God (Romans 1:9), (3) praying and singing to God (1 Corinthians 14:15), (4) our spirit is saved by God (1 Corinthians 5:5) and (5) our spirit belongs to God (1 Corinthians 6:20). For those of us who are saved our spirit goes to Heaven upon death (see Ecclesiastes 12:7, Acts 7:59, Luke 23:46) and our body and soul will be reunited with our spirit at the Rapture. Those who are still alive at the Rapture will be changed in the twinkling of an eye (see 1 Corinthians 15:50-57 and 1 Thessalonians 4:13-17). The body, soul, and spirit of both the living and deceased believers are given immortality and will be like Christ (see 2 Corinthians 3:17-18). It should also be noted here that the unsaved have a spirit as well. However, their spirit is dead, as they do not have a relationship with God (see Ephesians 2:1-5). When a person dies without Christ his body will return to dust (see Job 34:15) and his soul will go to Hell (see John 5:28-29, Revelation 20:11-15, and Matthew 10:28). His spirit was already dead since an unregenerate person is spiritually dead. This should help explain why the unsaved have a very difficult time grasping spiritual matters (see 1 Corinthians 2:14). They cannot communicate spiritually with God even though they are alive physically!
When God passed the judgment of death to Adam and Eve (see Genesis 2:17 and 3:16-17) it included the death of all three parts of man's being. When Adam and Eve sinned the first time, they immediately died spiritually. That meant they were separated eternally from God. Why? Remember, God will not be around sin because He is Holy! The death of the soul took more time. Since we are removed from the presence of God (until we are born-again) we become more degenerate as our evil nature takes over our thoughts. Note, this condition can happen to a Christian who is out of fellowship with God due to unconfessed sin in the Christian's life. Finally, the curse of sin eventually catches up with the body and we die physically. God created man's body to be the temple where He would dwell with man (see 1 Corinthians 3:16-17 and 2 Corinthians 6:16-17). So, when God passed a judgment of death to man for his sin, it was a judgment of all that makes up man's being (see Matthew 10:28). This is why we need to be "born-again" through Christ (see John 3:3). It is only through the new birth that we can hope to attain entry into Heaven as we are deemed righteous through Christ.