The Heart of the Truest Believer - S3-E1
Continuity mistake: After Neal wakes up on the bier, after he says "A .45 caliber arrow", Aurora's dress keeps alternating between having straps and being strapless between shots. (00:13:25)
The Heart of the Truest Believer - S3-E1
Continuity mistake: When Neal and Mulan are walking to Rumpestiltskin's castle, after Mulan says "Your belief in love wasn't strong enough to overcome your fear of rejection", her hair keeps changing. In close-ups, some of her hair is over her shoulders; in the wideshots, all of her hair is behind her shoulders. (00:23:00)
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.