I wrote a short program that reads data into a buffer (over USB, in my case) and then writes that data to the flash using the CFI flash device driver function alt_flash_cfi_write. Check the peripherals handbook on how to use the flash interface. If you don't want to write a whole sector at once (i.e. transfer a whole flash-sector's worth of data) you'll have to use the "fine-grained" flash interface.
Andrew
