using cy7c68013a with cyclone II

I didn't work with 68013a software myself. I have been involved in a hardware design that uses it, so I'm familiar with the basic concept.

If I understand right, you're design has been communicating through 68013a before, but you don't know how it was achieved in detail. For 68013a firmware, you have the option to load it either from the EEPROM or through the PC driver after attaching the device, in the latter case, the firmware image is included in the driver executable, I think. 68013a uses basically a 8051 processor core, I'm not sure, if Cypress has included a compiler with the design tools or if they are using an industry standard compiler.