The flash programmer uses its own SOF file when it's programming the flash. The base address specified on the command line here is the base address of your flash device in the flash programmer design.
See the flash programmer user guide
documents/ug_nios2_flash_programmer.pdf for more details.
If your design isn't working then you can step through the boot loader (which copies your code from flash to RAM) to see what's happening. In one Nios II shell you should enter:
cd <where your elf file is>
nios2-download --reset-target --tcpport=2342
and in another window:
cd <where your elf file is>
nios2-elf-insight <project.elf>
target remote :2342
This will all be easier in 5.0