I came across this excellent document on "How to form a Catholic conscience". You can read it at source or read it below.
Deep within his conscience man discovers a law which he has not laid upon himself but which he must obey. Its voice, ever calling him to love and to do what is good and avoid evil, sounds in his heart at the right moment... For man has in his heart a law inscribed by God... His conscience is man's most secret core and his sanctuary. There he is alone with God whose voice echoes in his depths.[i]
Conscience is not something that allows us to justify doing whatever we want, nor is it a mere "feeling" about what we should or should not do. Rather conscience is the voice of God resounding in the human heart, revealing the truth to us and calling us to do what is good, while shunning what is evil.
1. First, there is a desire to embrace goodness and truth; to do what is right.
This sounds very simple, but it’s not. Because of our fallen nature and the effects of original sin, we are often dominated by self-interest. We must make up our minds that we wish to do what is right and pleasing to God - not what is satisfying to ourselves. What does God desire? Does this reflect God’s love?
2. Trust in God, His Law, and His Church
In difficult matters of conscience, we may be tempted to claim that we can decide for ourselves what is right and wrong, and that we know better than the Bible or 2000 years of Church Teaching and Tradition. This, though, is arrogance, not wisdom. Jesus taught us: “If you love me, you will keep my commandments (Jn 14:15). Jesus also left us the Church as “the pillar and bulwark of the truth” (1 Tim 3:15), and He told us that by listening to those who teach in His name, we listen to Him (Lk. 10:16).
3. Study Sacred Scripture, Sacred Tradition and the official teachings of the Church.
We believe that God reveals Himself - His Truth - to us, by the power of His Holy Spirit, through Sacred Scripture, Sacred Tradition, and the teaching authority of the Church. To have a well formed conscience entails a serious study, attentiveness, and understanding of what God has revealed to us. We must be willing to listen to God, not just ourselves.
4. Use reason to examine the facts and background information about various choices.
"Though faith is above reason, there can never be any real discrepancy between faith and reason. Since the same God who reveals mysteries and infuses faith has bestowed the light of reason on the human mind, God cannot deny himself, nor can truth ever contradict truth”. Consequently, methodical research in all branches of knowledge, provided it is carried out in a truly scientific manner and does not override moral laws, can never conflict with the faith, because the things of the world and the things of faith derive from the same God. The humble and persevering investigator of the secrets of nature is being led, as it were, by the hand of God in spite of himself, for it is God, the conserver of all things, who made them what they are." (CCC, 159)
5. Seek the advice of good, wise and prudent people.
This is especially important when facing practical judgments of conscience. We must be careful to seek the advice of friends, clergy, or Religious who are faithful, prudent, well informed, and wise. The Church invites us to take our concerns to the Lord in a special way in the Sacrament of Reconciliation.
6. Finally, and most importantly, prayerful reflection is essential to discern the will of God.
The more we pray with humility before God, the better we will be able to hear Him speak in the depths of our hearts. Thus, a well-formed conscience is one truly sensitive to the voice of God rooted in His Word. If we sincerely desire to live in a manner holy and pleasing to God, we must ask for the help of the Holy Spirit, who will remain in us and lead us to all truth (cf. Jn. 14:16-17).
Absolute Guiding Principles: (CCC, 1789)
1. At times, more than one decision can be morally justified, but we “may never do evil so that good may result from it”.
2. Follow the Golden Rule, “Do to others, as you would have them do to you”. Charity always proceeds by way of respect for one’s neighbor and his conscience; therefore you should never do anything that may lead your neighbor to stumble and sin.