An Apple Red as Blood - S1-E21
Visible crew/equipment: After Regina walks into Gold's shop and tells him about the sleeping curse, just as she asks, "Don't you understand?" we can see the green tape mark (and its reflection) on the floor in front of the display case, where Regina is about to stand. (00:38:55)
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.