Hi,
I think, the older version of Nios II flash programmer allowed for the programming of FPGA configuration in EPCS memories, but the new versions don't. The new versions allow for only cfi flash memory programming for FPGA configuration data even with an EPCS controller instantiated in the system. I think you'll need to program both separately: Use Quartus II programmer to program the .pof file and use the Nios II flash programmer to program the .elf file. May be someone else can suggest a way to program the .pof file in EPCS memory through Nios II flash programmer, if it exists.
Cheers,
BD