You can't get both Nios cores to boot from the EPCS simultaneously. They will both try to access the EPCS at the same time and will probably get corrupted data back. You need to hold one CPU B in reset and boot CPU A. When CPU A is ready it can deassert the reset signal on CPU B so that it can boot. Will you run the exact same software on both CPUs? If you need a different software on CPU B, then you will need a custom bootloader for it so that it picks it up from the correct place in the EPCS. You can put this custom bootloader in an on-chip ROM and have the CPU B's reset vector set to that memory.