There are two ways that Christians could potentially make moral decisions - instinctively by examining their consciences or intellectually by asking themselves what they believe God would want, what the Bible says. The most natural way would be to use their consciences, just as non-Christians do, and I believe that most Christians do indeed follow this path. Christians and non-Christians alike, also take regard of the risk of breaking the law, when making some decisions of a moral nature.
Of course in more formal situations, such as business decisions , conscience may be supported by ethics training.