Configuring FPGA through EPCS (EEPROM) INCLUDING Nios II program?

Sure you can!

First of all you need to build a hex file including both fpga configuration and nios firmware.

From a nios shell window you need to send these commands:

sof2flash --epcs --input=fpga_project.sof --output=fpga_project.flash

elf2flash --epcs --after=fpga_project.flash --input=nios_firmware.elf --output=nios_firmware.flash

cat fpga_project.flash nios_firmware.flash > hw_sw.flash

nios2-elf-objcopy -I srec -O ihex hw_sw.flash hw_sw.hex

Then, in Quartus select File->Convert programming Files

Select JTAG INdirect Configuration File (.jic) at "Programming file type".

Select your EPCS configuration device model and write the desired output filename .jic.

In the bottom box select Flash Loader -> Add Device, and then select your fpga model.

If any sof line is already there, delete it; then select Add Hex data with the previously generated file.

Press "Generate".

I recommend to save the configuration (.cof) file, so you avoid to setup everything again when you need to generate a new version. You could also automate the shell commands in the beginning with a script file.