The epp file has to be stored in the EEPROM of the processor. This can be done using avrdude (-U parameter).
What do you expect the hardware to do at bootup? Pin 13 is used as the clock line so with a standard multimeter this pin will look HIGH when measured. Have you checked with a scope? It should communicate with the ENC28J60 intensively during the first 5 seconds, jumping then to the non-existing application code. Do you have networt traffic on the ethernet interface in this time?