You need to configure your Cyclone Pro with an image that contains both the algorithms for the flash and EEPROM.
CM 9S12dp256_4k.12P 4000 ; algorithm for eeprom
CM 9S12dp256_256k.12P ; algorithm for flash
Configure this image and load it into the Cyclone Pro using the Cyclone Pro Image Creation utility. When this is configured, you can just press the start button. The configuration script will be carried out in sequence in the Cyclone Pro.