boot multiprocessor from one EPCS device

In the QSYS advanced features tab for the NIOS processor make sure "Assign cpuid control register value manually" is checked (it should be checked by default). Use different values for your two processors (1 and 2 say). Give both processors the same reset and exception vectors.

In your code, read the value of the cpuid register. A different value will be returned depending on which processor is running. In other words, each processor has a cpuid register that you set in qsys. When your code reads that register, each processor will return the value you set for that processor in qsys.