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Thanks for your reply.
Does i require Serial EEPROM(93C46)chip or it can be ignored.
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Fully
integrated 1024 bit EEPROM storing device descriptors and FIFO I/O configuration.
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I can't see any way to connect 93C46 to FT245.
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Just all the Lines from FT245R is to be connected to Cyclone IV naa.
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D0-D7, RD,WR, RXF, TXE, PWREN. Maybe RESET. To Cyclone. Also you will need to programm this chip with FTDI utility.
It's simplest way to communicate with PC.