The technological development of the last decades resulted in the rise of entirely new paradigms in healthcare. Computer-Integrated Surgery (CIS) is providing innovative, minimally invasive solutions to heal complex injuries and diseases. It integrates robotic devices to the treatment delivery phase. By now, well over 6 million successful operations have been accomplished with various systems. In certain critical surgical procedures, where spatial accuracy is a must, physicians extensively rely on the help of CIS, and particularly on intra-operative navigation system. For these, the ways of use, including setup, registration and application accuracy metrics are provided by the manufacturers. Depending on the setup, inherent system errors can accumulate, and lead to significant deviation in position measurements. It is crucial to improve the precision of integrated setups, and to determine the overall task execution error. The stochastic approach proposed here offers an easy and straightforward solution to map and scale the error propagation. Applying pre-operative and on-site simulations, the optimal positioning of the navigation system can be achieved. This results in faster task execution and reduction of the probability of surgical errors. Surgical tracking systems have broader applications in endoscopic surgeries, and the method described in the article can be directly applied to these procedures too. It was tested in silico and on a neurosurgical prototype robot system developed at the Johns Hopkins University. The proposed features together can greatly increase the safety and reliability of all procedures where camera systems are involved, and ease the surgeon's task and potentially reduce operating time.