multiple NIOS II cores

It shouldn't be too much different then NIOS I (somewhere there is a document for NIOS I that gives a tutorial of how to do multiple cores in one SOPC). When/if you download the code over JTAG you need to tell it what you plan on targetting.

If you have 2 CPUs. Try memory for each core. Then once you get the hang of it you might be able to use the same code memory (if they run the same software that is).

What are you trying to do by the way?