The Heart is a Lonely Hunter - S1-E7
Revealing mistake: When Emma and Graham are chasing after the wolf into the graveyard, there is a shot where the wolf turns its head toward them, closes its mouth and perks up its ears, while growling. The wolf howls, before turning its head toward them again, and you can see that it is exactly the same shot that was used earlier, only this time, the wolf can be heard whimpering. (00:28:40)
Answer: He knows who she is because he knows that the fairy tales are true. He was also shown to sneak out to go see Emma or someone else. Sometimes he succeeded, sometimes he didn't. This is how he knew to look for her despite his strict mother.