Hi,
I just checked in newest Quartus v9.1 with the SOPC providing an EPCS serial flash controller, which as described shall provide the functions for NIOSII systems to connect to the EPCS.
"The EPCS Serial Flash Controller core enables Nios II systems to access an Altera EPCS serial configuration device connected to the FPGA.
Altera provides device drivers for the Nios II processor which allows you to read and write the EPCS from Nios II software"
This should do the job for NiosII based systems. I know there is also a VHDL module for systems w/o Nios II cores.
Nevertheless, using the EPCS storing the config as normal FLASH requires ensure not to write to the false address (changing the config data...) ;)