Shirley appears on the Sgt. Pepper album cover 2 or 3 times depending on if you count the doll.
Her image from the movie Heidi is obscured and sits between the wax figures of Ringo and John (you see just a little bit of her yellow hair poking out). She is to the left (looking at the album cover) of Diana Dors on the right hand side of the cover and of course the "Welcome the Rolling Stones Doll".
There is an excellent analysis of the cover and photo shoot here:
http://www.fab4art.com/sgt_pepper_shoot.htmand a listing of all the characters here:
http://math.mercyhurst.edu/~griff/sgtpepper/people.html