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.