cyclone iii nios boot from epcs

Correct !

In fact the FPGA Image is read byte after another so inside the EPCS some kind of actual adresspoint is set and incremented, after the last FPGA image byte, this pointer points to the first byte of the application software and the boot loader can fetch again one byte after another continuing the data stream.

So just ensure that your application is directly after the fpga image.

This means whenever you change your application, you need to assemble to complete EPCS image again.