To boot eCos from an EPCS you simply need to select a "ROMRAM" configuration for the "Statup type" in configtool. Assuming that you have configured the hardware reset vector in SOPC builder to point at the EPCS device, then this will build an elf file suitable for booting from EPCS.
The generated program_flash should also be able to happily program it into the EPCS for you. However it sounds like this isn't the case.
If not, an easy way to determine what options the script should have been using is to program a HAL "hello world" example into the EPCS using the IDE. YOu can get the command the IDE uses by going to the Windows->Preferences->Nios II tab and ticking the "Show command lines when running make" option. You can then compare this to the commands issued by the program_flash script.
If you find there is a discrepancy, please post the results back.