Yes, she was; but no, she didn't sit with the Royal family. Andrew sat to the left of William and Catherine, with his daughters on his left, and Eugenie's fiancé on her left, and then the friend of the famly, Mrs. van Cutsem.
I taped the wedding and was watching it. I thought I saw her in the Choir portion of the church on the same row as her 2 daughters and Prince Andrew. Maybe once the service started she moved.