This guide is written for Windows though will work with Linux with minor adjustments.
1. First install the Atmel Flip Software. Get the version with java if you don’t have the Java runtime.
2. Remove the 2 jumpers from your Xplain board that are normally installed when you get it.
3. Put one of the jumpers over PINS 1 + 2 on the JTAG USB. (Like shown in the picture below) This will allow you to enter the programming mode to flash the chip.
4. Now connect the board to your pc with your usb cable. Now find your device in device manager or it make come up with a box asking to install driver. Click Install manually then choose Show all devices and click next
5. Click Have Disk, then browse to C:\Program Files (x86)\Atmel\Flip 3.4.1\usb\
6. Select atmel_usb_dfu.inf
7. Choose AT90USB1287 from the list and let it install.
8. Now open up Atmel Flip software and select device at90usb162 from the little microchip in the top left.
9. Now click the usb icon and click usb, then click connect.
10. Load the hex file that was included in this zip and flash.
11. That’s it now just remove the device from your pc. Remove the jumper from pins 1 + 2. And connect it to your ps3. There should be no jumpers on any of the pins.
12. Turn on the ps3 and then quickly press eject.
13. If your light on the device changes from orange to green that means its worked.