The paper proposes an efficient methodology that allows to design smart deformable aeronautical configurations that are able to achieve pre-defined target shapes by adjusting the temperature of Shape Memory Alloy (SMA) actuators. SMA-based actuation finds extensive application in morphing concepts which are adopted in aeronautics to enhance the aerodynamic performance by continuously varying the geometry of the wing. A novel robust algorithm, developed for predicting the nonlinear response of the SMA-structure interaction problem is presented. The algorithm is coupled with an optimization method in order to predict the optimal structural and operational parameters with respect to target shapes of the controlled configuration. The design methodology presented in this study selects the design parameters of the problem at hand, i.e. the location of the actuators and the operating temperature, for given loading conditions. The proposed methodology is validated and demonstrated with three case studies, including the design of a real-world aeronautical configuration.