Hi,
The question here is "Are these two NIOS processors working separately?" If yes so there is no problem just include the two hex files and make sure you point to the correct address in the NIOS vectors, If you need to control there boot please follow the following multi-core nios example:
https://fpgacloud.intel.com/devstore/platform/17.0.0/Standard/multi-core-nios-ii-processors-reference-design-based-on-arria-10-soc-development-board/
This example uses a main processor to boot another three processors. This is very clear in this example how to boot NIOS II processor and to copy the code to it's memory.
Regards,