NiosIIuser:
I did use the hex from the NiosII. When you check the sdk, they give you a nios2_germs_monitor directory under the sdk directory. It contains a .s and a makefile. You just pass the start address and srec name to the makefile. I have a Parallax dev board. This board has some sort of Pic chip that monitors the RS232 port. When you launch the px.exe app from a command prompt, it sends the .rbf to its on board flash. It is really kind of cool. If you use the /P option it will always boot from your FPGA data file, but you can send a new one at any time.
Rick