Cyclone IV and Nios II Firmware Update

The bootloader is part of the EPCS controller integrated in the SOPC/QSys system. Just point the Nios CPU's reset vector to the EPCS controller and the bootloader will load the .elf file from the flash. The bootloader will jump over the .sof image, so the .elf just needs to be placed after the FPGA image in the flash.

What file format are you using when you send data to your application, and how do you write it to the EPCS? The easiest format is probably .rbf, but IIRC with the EPCS flash you need to revert the bit order of every byte before you write them.