Pills- when am I protected?

I'm confsued. My Dr put me on Norg ee (generic of ortho try cyclen lo) and she said I could start the pill immediately (I have irregular periods and missed my period for July) but the pills won't protect me from pregnancy until a few months later. The pamphlet said it should take, longest, 7 days. What?! I'm so confused... this is my first time taking bc pills and tomorrow will be my 3rd day.