Programing atmega card

Hello Colin.
i want to work with a sasebo-w and i want to program my OS on atmega card. but i don’t know how! can you help me?
more detail: i want to program a “DES” algorithm instead of “AES” that is default on this card. but i don’t know how can i write this program and generate hex file. Should I re-programmed eeprom? can you tell me the roles of eeprom in card and the rom in fpga and what is the exactly in this memories?