Can the fpga read/write EPCS?

Yes, NIOS can. You need to add an 'epcs_controller' module in SOPC-builder. Altera docu 'Nios II Processor Reference Handbook' describes in chapter 12 how to do this and gives further links to HAL software usage.

In my design the first blocks contains the FPGA configuration data and boot software. This occupies less than 4 blocks of 64k each (out of 8 in an EPCS4). The last block in device is used for storing serial number and alterable config data.

Mike