How to build a two processor system?

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Yes. RTOS would allow you to spawn several threads. You can manipulate a thread to resume, suspend etc while the other thread executes. There is lot of helpful literature available for the RTOS that have been ported on NIOS eg. uC/OS-II.

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However, the tasks rely on RTOS would be much slower, it uses the RTOS system resources, the remaining resources would be wasted.

So the multiprocessor distributes system resource, would be much faster.