Step 12: Programming With the Arduino Uno
To program the chip with the uno board, I simply pried the chip on the arduino board off, and replaced it with the new chip. I then uploaded whatever sketch I wanted to use the same way you would any other. Once program I pried it out again and placed it in the new arduino board.
Anything you can do with the arduino (except serial read, and other things that require constant interface with the computer) can be done on the Homemade arduino in this way.