I'm following everything in the app but my daughter was born 6 weeks before her Estimated delivery date. Should I be using her birthday or her EDD?

As a guide, you should be using her EDD. However, I have a friend whose baby was born 4 weeks early, she noticed that her baby seemed to go through her leaps somewhere in between the predicted (based on EDD) dates and her actual birthday. So I think you may expect your girl to be somewhat similar. She may go through a leap slightly earlier than the predicted dates.