Parikshit is Manipal University's first 2U class Nano satellite mission. The command and data-handling department is developing the computer architecture for the satellite missions that have multifaceted requirements. The satellite is carrying a thermal camera as the payload for obtaining thermal images of the Indian subcontinent. With the space being a dynamic environment, it is required from an autonomous system to be robust and redundant. The system is expected to perform activities in real time, and with utmost precision given to computations and ability to recover from failures. In such systems, data handling and power management is a vital aspect to mission life. The computer acts as the brain of a satellite, which is expected to operate at constrained resource environments. A real time operating system is used in such cases where deterministic execution is of prime importance. This paper describes how the real time operating system is ported to an STM32F207 to control the satellite's mission life. A comparative study of how this RTOS is best suited for our mission is also presented. The RTOS is specifically designed to effectively manage power in this dual controller system. Results of 14 orbit simulation for control and attitude determination algorithms are also shown. The software design here is expected to monitor and control the execution of both the on-board controllers. The design of the software will be compatible with other university missions as well because most of them base their design on similar hardware bus. An analysis of the software execution on the Parikshit mission is described and results show how the chosen R TOS performs on a dual controller based system.