Continuity mistake: When Mr. Gold brings the town charter to Mary Margaret's apartment, he puts the binder on the table twice; once before he sits down, and then again after he sits down. (00:19:10)
Continuity mistake: When Emma goes to get the fire extinguisher, Regina grabs Emma's arm at the elbow. In the next shot, she's gripping Emma's wrist. In the following shot, she's gripping her elbow again. (00:22:25)
Continuity mistake: When Regina is on the stretcher, she has a yellow coat around her shoulders. As she pushes Sidney away, the coat has vanished into thin air. (00:23:50)
Continuity mistake: In the scene where Morraine is conscripted into the army, as well as the scene where the knights find Rumplestiltskin and his son on the King’s road, Rumplestiltskin's hand repeatedly moves up/down his staff between shots. The same thing happens to Baelfire in the scene where he and his father are preparing to leave for the Duke's palace.
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.