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Potentially, your processor can control everything from maneuver and power through to data gathering and transmission. You do have a processor budget—how many operations per second it can run. You also want a bulletproof mission, which suggests as little processing as possible to ensure that your programs are simple, debugged, and only used when needed.
Therefore, I recommend you not use computer commanding of your power system, but rely on good power architecture. Your primary use of the processor is for three purposes: data handling, turning your radio on and off, and commanding any engineering tests.