The extrusion-based additive manufacturing (AM) processes are those where one or multiple tools (usually nozzles) are driven along predefined paths to deposit fabrication materials. They are usually inherently slow because solid contours have to be filled with mere single deposition lines of material. An intuitive way to improve the fabrication speed is to introduce multiple independent actuators for concurrent deposition of materials without collision among them. In this paper, a methodology of using augmented reality (AR) technique is presented to conveniently communicate the layout information between a reconfigurable AM system made of robotic arms and its corresponding digital twin for toolpath planning and simulation. A prototype system made of two desktops AM robotic arms is developed, and transformation matrices are derived to determine the spatial relation between different items in the system, including camera, markers, robotic arms and part substrate. Case studies are conducted to demonstrate the capability of this methodology in automatically retrieving layout information and assisting users to deploy pre-determined layout. The results show that the developed methodology enables rapid retrieval of position information from the physical system layout into the digital twin simulation and optimization and facilitates convenient deployment of an optimized layout determined in the digital twin into the physical system.