To FvM,
I apologize for the vagueness of the original wording of the question. After powering firmware must be loaded into the FPGA (AS or PS) and then external microcontroller can access the flash (in most cases is the checksum and comparing it with the standard). In indirect access, imho, FPGA is a transit device and is not fulfilling its direct functions. The essence of the matter, if translate the FPGA firmware in hex ​​format and program the flash XC18V00, connect D0 (XC18V00) with DATA (CYCLONE), CLK (XC18V00) with CLK (CYCLONE), etc. - understand whether the FPGA is a mockery?