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Quartus Prime does not handle c compilation. You can use the Eclipse tools for building the firmware or any other c project management tool. marqs85 e.g. uses Codelite and provides workspaces for that.

Interaction workflow between hardware and software is:
– hardware provides NIOS2 softcore and BRAM for the program
– program is initialized with content which has to be generated with nios2eds tools (default location is software/sys_controller/mem_init/sys_onchip_memory2_0.hex) <- this is needed to see your changes if you reinitialize the FPGA
– in runtime you can download new NIOS2 programs (default location is software/sys_controller/sys_controller.elf) to the NIOS2 core with nios2-download -g –accept-bad-sysid sys_controller.elf

Some links regarding this: