This paper presents a conceptual applied geographic information system (AGIS) for modeling search correlation-extreme navigation systems (CENSs) to control moving objects. As demonstrated below, the development and mass implementation of autonomous navigation systems of this type as the only alternative to satellite navigation systems can currently be based on subject-oriented information technology. The AGIS can be used to assemble models of a wide range of CENSs and models of technologies for adjusting their operation in specified areas with necessary computational experiments. The required software components, storage structure, and interface features are determined by constructing a general mathematical model. While preserving all specifics of the search algorithms of CENSs, this model covers the well-known image combining algorithms and, moreover, includes a synthesis scheme for search algorithms of newtype CENSs using pattern recognition and scene analysis, clustering, neural network training, and cloud data processing. Stress testing is the most important type of computational experiments with CENS models. A mathematical model of stress effects is constructed for a particular case. It describes various operating conditions for CENSs, including fatal deviations from normal operation.