Cyclone IV and Nios II Firmware Update

Thank you very much for all your replies. I have tried the default method (using the default EPCS bootloader).. But it seems after reset, the hardware is booting up properly but the software does not run. At this point i want to ask a question regarding the "--after" tag in the elf2flash command. Do i really need to use it, even when I concatenate both hardware and software firmware in to one file before downloading. It makes sense with the Nios2-flash-programmer, since the files are being written seperately.. Do i really need it if I am going to have only one file??