Coming to terms with death
One important moment on the boy's quest is the second trip to Mexico when he is attacked by bandits for trying to reclaim the bones of his dead brother. What does he learn about death? He learns that death is final, and life is precious and fragile. The gypsy woman who helps heal his horse is a deathly image as well—representing the balance between death and the mystic force of life.
Making sense of religion and philosophy
Billy treats every person as if their points of view matter. Compare that to a fundamentalist religious person who constant invalidates other people's religious experiences because they "have the wrong religion." That's the question Billy is struggling with when he meets a Catholic man who explains that, having belonged to two complete different sects of Christianity, he discovered that ultimately, the similarities matter more than the differences. There is one story, and every human narrative is a variation on that theme—including religion itself.
Conducting yourself dutifully
As a bildungsroman, the novel focuses on orienting the character to reality. Throughout the quests, Billy experiences new situations, but each time, he conducts himself as if he is responsible to improve the situation and conserve life, but that's not always easy, and his coming of age is only complete when he commits an act of evil, rejecting the wounded animal, and then learning the emotional recompense for making the wrong decision. We leave the character, now fully alive and adult, weeping bitterly over his sins and his difficult life. He is for the most part, an extremely honorable, dutiful person.