In determining what is right and wrong, conscience doesn’t work by magic. You first have to form your conscience. This means learning about good and evil, and that’s the job for the intellect.
Many people mistakenly think that conscience is the faculty that tells us what is right and what is wrong. Conscience is better thought of as an alarm. With your intellect you learn what’s right and wrong, and then conscience “sounds off” when you are about to violate the standards your intellect has learned. If you have no standards, you’ll never hear the alarm.
But you need to make sure not just that your conscience is formed but that it is formed correctly. If it is, the moral judgments you make will be reliable. If your conscience is formed poorly, then your moral judgments won’t be trustworthy.
For example, if you’ve been taught that there’s nothing wrong with stealing—or if you’ve never been taught that stealing is wrong—you won’t have any inhibitions against stealing. Your conscience won’t bother you when you steal because it isn’t reliable when it comes to the immorality of stealing. In other words, it’s been formed—but formed incorrectly.
It’s true we have an obligation to follow our conscience, even a poorly formed or “erroneous” one, but we also have an obligation to form our consciences properly. For Catholics, this means following what Jesus teaches in Scripture and Tradition through the magisterium of the Church.