two comments:
1. the serial flash interface changed from Quartus II 5.0 to 5.1 (and stays the same til now 6.1) you should use a newer version of Quartus
2. now EPCS_controller is the default interface (no need for anything else) to the serial configuration flash, with it it is possible to:
- program the hardware and software into EPCS flash from JTAG (from the Nios IDE or using command line tools)
- program the EPCS flash from software running on the Nios, there are drivers included in the SOPC component
The Epcs controller is constructed from a small boot ROM and a SPI interface to the serial flash. A good start point for flashing EPCS is the Nios IDE, you can later modify the flashing script created by the ide to learn more about command line flashing tools.
There are some problems with the flashing interface on the 6.1 version of the ide, check some older posts about workarounds (they involve changing the board description name).
IzI