In recent years, in-mold electronics (IME) technique was introduced as a combination of printing electrically functional materials and vacuum plastic forming. IME has gained significant attention across various industries since it enables various electrical functionalities on a wide range of 3D geometries. Although IME shows great application potentials, hardships still exist during design for the manufacturing stage. For example, printed 2D structures experience mechanical bending and stretching during vacuum forming. This results in challenges for designers to ensure precise circuit-to-3D mold registration or to prevent over deformation of circuit and attached components. To this end, we propose a software toolkit that provides real time 2D-to-3D mapping, guided structural and electrical circuit design with interactive user interface. We present a novel software-guided IME process that leads to fully functional 3D electronic structures with printed conductive traces and assembled surface-mount components.