A new design approach of complex geometries such as wing/body configuration is arranged by using overset mesh techniques under large scale computing environment. For an in-depth study of the flow physics and highly accurate design, several special overlapped structured blocks such as collar grid, tip-cap grid, and etc. which are commonly used in refined drag prediction are adopted to consider the applicability of the present design tools to practical problems. Various pre- and post-processing techniques for overset flow analysis and sensitivity analysis are devised or implemented to resolve overset mesh techniques into the design optimization problem based on Gradient Based Optimization Method (GBOM). In the pre-processing, the convergence characteristics of the flow solver and sensitivity analysis are improved by overlap optimization method. Moreover, a new post-processing method, Spline-Boundary Intersecting Grid (S-BIG) scheme, is proposed by considering the ratio of cell area for more refined prediction of aerodynamic coefficients and efficient evaluation of their sensitivities under parallel computing environment. With respect to the sensitivity analysis, discrete adjoint formulations for overset boundary conditions are derived by a full hand-differentiation. A smooth geometric modification on the overlapped surface boundaries and evaluation of grid sensitivities can be performed by mapping from planform coordinate to the surface meshes with Hicks-Henne function. Careful design works for the drag minimization problems of a transonic wing and a wing/body configuration are performed by using the newly-developed and -applied overset mesh techniques. The results from design applications demonstrate the capability of the present design approach successfully.