Hi what reference area should i use in calculating cn ca cm in case of rockets will its crosssectional area work and should i use half of its value when im using half body and using symmetry boundry condition

It does not matter if you use half the value or full value. The result is changed by a constant factor. See how experimental results are presented and use the same scaling so that you can compare them. I dont know if cross-sectional area is the relevant quantity for your problem.