hi ninjaben,
you could upload to FPGA NIOSII project with flash controller and write flash by nios2-flash-programmer
#
# programmin USER0 FPGA configuration
# SW2[0..2] = close, SW2[3] = open, SW2[4..8] = n/d.
#
# convert .sof to .flash file
sof2flash --input=my_sof.sof --output=my_sof.flash --offset=0x00900000
# write flash
nios2-flash-programmer --base=0x01000000 --program my_sof.flash
startix ii ep2s60 kit offset is a 0x00500000 (not sure, check docs)
startix ii ep2s180 pro kit offset is a 0x00900000
-- base means base address of the flash controller in the sopc-system.