Glueing before Sewing
Lay out the inner flaps onto the wrong side of the cover, blanketstitched edge facing inwards, and then let some glue do the trick before you are going to turn it over and blanketstitch the two layers together.
Using pins to keep the inner flaps in the right position while sewing from the upper side of the cover would damage the raw edges because the pins would have to go through four stiff layers of fabric/interfacing and cause much bending/fraying.