Yes, while applying for courses you need to order the courses as per your choice.
Same branch will be displayed 3 times along with its campus name if the course is offered in all 3 campus.
Ex:
B.E(Hons). Mechanical Engineering, Pilani Campus
B.E(Hons). Mechanical Engineering, Goa Campus
B.E(Hons). Mechanical Engineering, Hyderabad Campus
So based on full course name & campus you will be sorting your choice of courses.
Hope it helps !!