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The Autonomous Multi-Agent Physically Interacting Spacecraft (AMPHIS) test bed examines the problem of multiple spacecraft interacting at close proximity. This thesis contributes to this on-going research by addressing the development of the software architecture for the AMPHIS spacecraft simulator robots and the implementation of a Light Detection and Ranging (LIDAR) unit to be used for state estimation and navigation of the prototype robot. The software modules developed include: user input for simple user tasking; user output for data analysis and animation; external data links for sensors and actuators; and guidance, navigation and control (GNC). The software was developed in the SIMULINK/MATLAB environment as a consistent library to serve as stand alone simulator, actual hardware control on the robot prototype, and any combination of the two. In particular, the software enables hardware-in-the-loop testing to be conducted for any portion of the system with reliable simulation of all other portions of the system. The modularity of this solution facilitates fast proof-of-concept validation for the GNC algorithms. Two sample guidance and control algorithms were developed and are demonstrated here: a Direct Calculus of Variation method, and an artificial potential function guidance method. State estimation methods are discussed, including state estimation from hardware sensors, pose estimation strategies from various vision sensors, and the implementation of a LIDAR unit for state estimation. Finally, the relative motion of the AMPHIS test bed is compared to the relative motion on orbit, including how to simulate the on orbit behavior using Hill's equations.