The Duemilanove and likes has hardware to connect the Arduino to the PC:s USB-port. When you build a clone you usually dont add hardware for this. Instead one might use a FTDI-cable, or why not a Duemilanove? I have one for prototype building, and it can be used for programming the clones to. -Remove the Atmega from the Duemilanove. -Connect the Duemilanove to the clone: Duemilanove <-> Atmega based clone: Reset -> reset(pin 1) 5V -> Vcc(pin7,20) Gnd -> GND(pin 8,22) RX -> RXD(pin 2) TX -> TXD(pin 3) Then just program the clone as usual.