Sorry for the late response. She debuted in the New Teen Titans era so I'm cool with her and Mal sticking with them. Granted her knowing Jason as Robin is more interesting because you could explore how she would react to her friend becoming a villian.
You could always have it be an informal apprenticeship- he trains her because he's the Atom and she's a new hero. Eventually she might decide to go to his college to continue the apprenticeship in a formal setting. He might inspire her to be a certain type of scientist or whatever.