Can the fpga read/write EPCS?

Yes, there is a way, but this is the Nios forum so you may do better asking in other places.

My suggestion on how to proceed is to install the Nios II kit and look in one of the example designs, for example the 1c20 full featured design. In the verilog for the EPCS controller there is a module called tornado_epcs_controller_atom which looks as though it has the right pins on it. If you try instantiating one of those in your design then it will probably be connected up correctly by Quartus II.