Stacking refers to the act of adding together bonuses or penalties that apply to one particular check or statistic. Generally speaking, most bonuses of the same type do not stack. Instead, only the highest bonus applies.

Most penalties do stack, meaning that their values are added together. Penalties and bonuses generally stack with one another, meaning that the penalties might negate or exceed part or all of the bonuses, and vice versa.

Many traits grant a new type of bonus: a “trait” bonus. Trait bonuses do not stack—they're intended to give player characters a slight edge, not a secret backdoor way to focus all of a character's traits on one type of bonus and thus gain an unseemly advantage. It's certainly possible, for example, that somewhere down the line, a “Courageous” trait might be on the list of dwarf race traits, but just because this trait is on both the dwarf race traits list and the basic combat traits list doesn't mean you're any more brave if you choose both versions than if you choose only one.