Systems which transform optical wavefronts into digital information for imagery or machine interpretation lack suitable design tools and methods. In Wavefront Coded imaging systems in particular, the signal processing and the optics must be jointly considered to achieve an optimal solution. Computational imaging systems have recently been designed at CDM Optics based on human interpretation of images and guided by machine (algorithmic) interpretations. CDM is generating an integrated design package called WFCDesign to provide for truly joint optimization of computational imaging systems where both physical and algorithmic goals can be jointly realized with a high degree of efficiency and accuracy. WFCDesign interfaces to a multitude of commercial analysis, design, signal processing, and simulation packages, enabling joint optimization using industry-standard tools. Methods for approaching the optimization problem including merit functions and optimizer issues are discussed. An example of a computational design with Wavefront Coding based on a digital algorithm's performance (as opposed to strictly optical metrics such as spot size or aberration curves) is provided. An outline and discussion of the WFCDesign package highlights the capabilities of our flexible approach and modular architecture and provides insight into the future of computational imaging design tools.