The text for Endless Hatred says it increases favored enemy bonuses by 2. I just want to make sure that this is treating favored enemy as one level higher(+2/+2) rather than two(+4/+4).
The BONUS increases by two. Not by two steps up the scale. So if your bonus against, for example, Dragons is +6, it now becomes +8. And your other bonuses against other things also go up by +2 since it affects all your favored enemies.