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=0x800000 --pfl --optionbit=0x00018000 --programmingmode=FPP
elf2flash --base=0x00000000 --end=0x03FFFFFF --reset=0x23C0000 --input=yourfile_sw.elf --output=yourfile_sw.flash --boot=$SOPC_KIT_NIOS2/components/altera_nios2/boot_loader_sources/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%.