The automation system of the future will consist of an increasing amount of complex resources, such as collaborative robots and/or autonomously roaming robots for material handling. To control these devices in an environment shared with human operators require state of the art computer perception and motion planning algorithms to be used as part of the automation system. This new type of intelligent automation system, where intelligent machines and learning algorithms are replacing more traditional automation solutions, requires new methods and workflows to keep up with the increase in complexity. This paper presents an interactive and iterative framework for solving some of these new challenges. The framework supports model-based control system preparation performed simultaneously to preparation of 3D geometries, positioning of robots, and tool design. The workflow enables an interactive preparation process, where new resources and constraints can be added to a live (real or simulated) automation system and control system failures can be analyzed in familiar tools for virtual preparation. Additionally, the paper describes how the integrated preparation process was applied to reconfiguring an industrial use case that includes a collaborative robot working side by side with a human operator, smart tools, and a vision system for localizing both work objects and tools.