Additive manufacturing of microoptics using two-photon-lithography has been a rapidly advancing field of technology. Striving for ever more sophisticated optical systems prerequisites the access to appropriately fast and accurate wave-optical simulation methods to predict their optical performance. A simulation routine, which has been proven well suited for simulation of a vast range of 3D-printed microoptical systems, is the wave propagation method (WPM). Nevertheless, limitations in applicability remain due to the restriction on scalar electromagnetic fields, which prohibits consideration of polarization and thereby also the calculation of backward reflection at optical interfaces. Capabilities for design and analyses are, therefore, impaired for 3D-printed optical systems using those properties as key features in their design. As a first step to overcome those limitations, we presented new simulation methods based on the WPM in previous publications, extending its applicability toward simulation of vector electric fields, while maintaining short-simulation runtime. We focus on elaborating the practical application and integration of previously presented simulation methods in the design of complex 3D-printed optical systems. With it, we demonstrate the consideration of polarization and backward reflections in simulations far beyond paraxial and thin element approximations.