Cyclone IV and Nios II Firmware Update

About your first question, the software should be written into the flash just after the FPGA image. AFAIK the bootloader isn't block aware, and will just get the FPGA image size from it header in the first few bytes, jump over it and start reading the elf image.

For your second question there isn't any significant difference in that area between the Cyclone III and IV so it should work. I have several projects here on Cyclone IV with the standard EPCS boot loader and they boot fine.