Yes. Spirit, soul and body work together. But what governs us should be the spirit, with the soul and body responding to the leading in our spirit man. It is important to know the truth. Many believers are ruled by thought and feeling and not by the witness in their spirit. This leads to people doing "good" (in their estimation) and not doing what is right before God.
Yes, what governs us is the spirit, and when we repent, what governs our spirit is the HS as we cooperate. I explain it thusly:
With greater awareness because of learning the NT Gospel, when a truthseeker confesses Jesus as Messiah and Lord (Acts 20:21, Rom. 10:9),
the HS indwells the convert’s heart (Rom. 5:5) and unites him/her with God as heavenly Father (Rom. 8:9)–which moment is called spiritual rebirth (John 3:3-8), baptism by the Spirit (Matt. 3:11/Mark 1:8/Luke 3:16, John 1:33, Acts 1:5, 1Cor. 12:13) and receiving the Spirit of adoption/sonship (Rom. 8:14-16). The outward evidence that someone was baptized by the HS (Rom. 5:5) and is Spirit-filled (Eph. 5:18) or walking with God is the fullness of Christ (Eph. 3:19, 4:13) or fruit of the Spirit (Gal. 5:22-23), which is
signified by “love” (Gal. 5:6). Jesus said “All men will know that you are my disciples if you love one another” (John13:35, 1John 4:7-21), because divine love sums up the moral character of God (1John 4:7-8).
The personal relationship between Believers/Christians and God may be viewed as having three stages: conversion, spiritual growth or maturation (Eph. 4:13), and glorification (1Pet. 5:10) or immortality (1Cor. 15:53) in heaven. The kerygmatic prayer that is necessary in order for a sinner be saved and walk with God is confession (1John 1:9, Psa. 32:1-5). Because a convert’s commitment to Christ is in accordance with God’s perfect will (1Tim. 2:3-4), the moment of Spirit baptism fulfills the command to be filled with the Spirit (in Eph. 5:18), which means to cooperate fully with the love of God (Eph. 3:16-19) or of the HS (Rom. 15:30).
The moment or stage of
conversion may be described grammatically as occurring in the past: we were saved when we repented/received the baptism of the HS. From the moment of repentance onward begins the second stage of growth, discipleship (Acts 14:22) or
sanctification (2Thes. 2:13), which is present progressive: it is the process of being saved now. This stage has two phases: instability and maturity. A new convert does not achieve immediate perfection by remaining filled with the HS (Phil. 3:12). Instead, the combination of temptations, ignorance of GW and the old selfish nature results in immature saints committing post-conversion sins, at which time the are carnal or acting like unbelievers (1Cor. 3:1).
As soon as new Christians realize they sinned, they should
confess it (1John 1:9a) rather than compound it by trying to hide it or cover it up like Adam and Eve did (Gen. 3:7-8). Whenever a believer acknowledges to God his/her known sins of immoral attitudes and actions, God forgives all sins (1John 1:9b). This means he/she is pleasing rather than grieving God or once again is
Spirit-filled (walking in the Spirit) and has a right relationship with Christ Jesus (Eph. 4:30, 5:10 & 18). This spiritual flip-flopping is the phase of instability, and although it is bad, failure to confess promptly is much worse, because it results in chain-sinning or back-sliding, which may be called prodigal if it continues very long (cf. Luke 15:11-32).
Unfortunately, some saints may not appreciate the process of spiritual growth or being transformed by the renewing of their minds (Rom. 12:2), perhaps because it involves admitting sins or having “guilt trips”.
Guilt is like a warning light, and until we gain the wisdom to welcome God’s reproof, we will not feel the satisfaction of becoming a new and improved version of ourselves (Heb. 10:19-22). Thus, guilt is good (John 9:41). Woe to the one who become so callous that no guilt is felt when wrong is done (Matt. 13:14-15)!
The unstable phase is followed eventually by
a second phase in a believer’s relationship with God’s HS of relative maturity, signified in the Bible (especially the KJV) by the phrase “
walking with God” (cf. Enoch in Gen. 5:24) or walking in light (1John 1:7). Paul also described this phase as walking in love (Eph. 5:2), in a new life (Rom. 6:4) according to the Spirit (Rom. 8:4) and in good works (Col. 1:10).
Like physical walking, spiritual walking has
two steps. The first step is listening to God (LGW), and the second step is responding to or cooperating with God. God’s message for mankind is revealed partially by the world He has created but more fully by the Scriptures He has inspired. The crux of God’s Word is the Gospel of salvation (
kerygma), while the secondary teachings (
didache) consist of the manifold applications of the law of love (1John 3:11). The Believer’s main types of responses to God’s Word are prayer to God and good works unto others for God (cf. 1John 4:20, Eph. 2:10).