I found this article to address very satisfactorily a question that has occurred to me on more than one occasion (see first paragraph for the question):
How can it be simultaneously true that Catholics must follow their consciences and that Catholics must follow Church teaching?
First, we must understand that the conscience is not equivalent to our thoughts or our opinions or our judgments. The Catechism (No. 1776) defines the conscience as an inner sanctuary in which we listen to God’s voice for guidance about our actions. So when someone is consulting his or her conscience, the question being asked is not “Do I think this action is good or bad?” but “Does God judge this action to be good or bad?” And God speaks to the consciences of Catholics through the Church.
If a Catholic is considering doing something that the Church teaches to be wrong, he can be certain that he is not listening to his conscience, but some other “voice” that has caught his attention.
So following our consciences does not mean doing what we judge to be right, but rather doing what we believe God judges to be right.
I am extremely grateful for the clear voice of the Catholic Church. I would be lost without it.