What is the relationship between the soul, conscience, reason and God?
The soul and conscience are one in the order of being but conscience emerges with consciusness. Conscience emerges with with brain development, but conscience, as such, is a primordial datum embedded in the soul which dictates that good is to be done and evil avoided.
Conscience does not originate in the feelings although feelings may be involved in moral decisions. "Conscience makes something obligatory to your choice , no matter how your appetites feel about it." Conscience lies in the order of primordial knowledge. Nor does conscience originate with society because conscience of individuals, at times, go against the common moral sense of the many. "Conscience is an aptitude, faculty, intuition or judgment that assists in distinguishing right from wrong." (wikipedia/Conscience) From a psychological viewpoint the violation of conscience often leads to feelings of remorse while obedience to conscience gives way to feelings of rectitude and integrity. (Ibid.)
In the ultimate analysis, conscience is the Voice of God in the soul. It is "The interior space in which we can listen to and hear the truth, the good, the voice of God. It is the inner place of our relationship wit Him, who speaks to our heart and helps us to discern, to understand the path we ought to take, and once the decision is made, to move forward, to remain faithful." God is absolute goodness who knows what is contrary to his goodness and who speaks to our hearts with authority.
This is not to say that conscience is always right because the judgment of conscience can be influenced by emotions, upbringing, bad habits and social ways of thinking and acting which are contrary to God's law. This means that reason plays its part in the formation of conscience. God has externalized the primary dictates of conscience in the "Ten Commandments" to help us clarify our conscience. We also look to the authority of Christ and his Church to tell us what is right or wrong especially when dealing with remote conclusions of the natural law, (e.g. contraception is always wrong).