From the Start Menu select All Programs, Altera, Nios II EDS, and then Nios II Command Shell
sof2flash --input=yourfile_hw.sof --output=yourfile_hw.flash
--offset=0xC80000
elf2flash --base=0x0 --end=0x0FFFFFFF --reset=0x03540000
--input=yourfile_sw.elf --output=yourfile_sw.flash
--boot=$SOPC_KIT_NIOS2/components/altera_nios2/boot_loader_cfi.srec
Browse to the hardware file and the software file (if required), respectively.
Click Upload, and then wait for the files to be written to flash. Progress is displayed from 0 to 100%.