The two abilities are independent from one another. You get the bonus anytime you make a knowledge check related to the creature type. So, for example if your favored enemy is goblin. You would get the bonus on knowledge history when trying to determine the history of a nearby goblin tribe. You would get the bonus on knowledge nobility when trying to determine what you know about the goblin tribe's political structure.
Independently of this if you see a weird looking goblin you can make a knowledge local check to identify it as a hellion arctic goblin even if you aren't trained in knowledge local and even though the DC to identify it is higher than 10. (knowledge checks can normally be made untrained but only against checks with a DC of 10 or less)
LordKailas is correct about the bonus applying to any knowledge skill relating to your favored enemy. But the only thing you are allowed to do untrained is to identify the creature. So if you have not ranks in knowledge local you can use that untrained to identify a human. But if you don’t if you are untrained in knowledge history you still don’t get to roll that even vs a human unless the DC is 10 or less.
If you have ranks in the appropriate knowledge skill you always get a roll even if it does not apply to your favored enemy, you just don’t get the bonus. So if you are trained in knowledge local you can use it for anything it covers. If you the subject of your questions are human you get the favored enemy bonus in addition to your normal bonus.