What to do after prototyping? I want to make a USB gamepad, and I've heard that an Arduino would be great for this kind of project. But before I start to work on it, I want to make sure I understand some things. Here are my basic diagrams of what the project will look like during prototyping and after prototyping:







Do the diagrams look right? Am I understanding the process correctly? For me to properly build a final circuit, I would have to emulate all the necessary (the most important one being the USB) circuitry that an Arduino has around it's microprocessor.

And my final question is, how would I load my program on to the microprocessor (with and without the "Arduino-like" USB circuitry)?
Yes, your thinking is pretty much correct.

You can place an ATMega32U4 chip and the associated required circuitry within your own circuit design. The required circuitry is actually quite simple - a crystal for the CPU clock, a few capacitors (load capacitors for the crystal, and decoupling), two 22Ω termination resistors for the USB bus, and a 10KΩ pullup on the reset pin. That's about it (besides power of course).

As far as programming goes, you can either install a bootloader (butterfly - like the Leonardo etc) that works through the USB, or you can directly program the chip using ICSP. It's best to provide an ICSP header anyway (it's the SPI pins plus RESET basically), and if you have done that (which you'd need really to be able to get a bootloader on there) then you may as will skip the bootloader entirely and just program direct through the ICSP header. Of course, you'll need some kind of programmer (an Arduino can do the job at a pinch, but it's worth spending the $10 to get a cheap AVR programmer from eBay).