So there is NO way of feeding data into the EEPROM through FTDI? I need to accept that... 
May there is a back-door. Here is my idea:
I send the following to the Arduino through the USB: 4711 12 5
Arduino send the confirmation back sending: 12 5
Arduino interprets 4711 as command for writing into the EEPROM. And the values to be written would be 12 and 5. May a mor unique number than 4711 would be good...