In general, bonuses from the same (or a very similar) source do not stack with each other. Penalties, however, do stack with each other. Bonuses with the same name never stack.
For example, if you have two +1 Innate bonuses to Knowledge, you only get +1. If you had a +2 and a +1 Innate bonus, you would get +2. If you had a +1 Innate bonus and a +1 circumstance bonus, they would stack to be +2.