Pi AVR Programmer HAT Hookup Guide
QCPete 
ISP Programming: Stand-Alone (aka Headless)
In this section, we are going to program using the Raspberry Pi "headless" (aka no monitor, mouse or keyboard). We will use the built in capacitive touch pad to engage programming and status LEDs to indicate success or failure. For this example, we will program the Arduino optiboot bootloader onto the RedBoard.
After you have setup your raspi for use with the Pi AVR Programmer HAT, then there are two important things to consider while using it as a stand-alone programmer:
Your hex file -- This should live in the '/home/pi' directory.
pi_program.sh -- This shell file contains all the settings for programming and can be edited with any text editor.
If you are plugging into the 2x3 header on a different AVR target IC, then we do recommend double checking that you have the polarity correct. The _pin 1_ is usually marked with a line of silk (as on the adapter), but it can also be indicated by a different style pad (usually square vs round).
After your setup and powered, programming is a simple as 1-2-3:
To engage programming in stand-alone use, simply tap the capacitive touch pad labeled, "TAP TO PROGRAM".
The STAT LED will go solid during programming. This can take a couple seconds -- depending on the size of your hex file.
Finally, the SUCCESS and FAIL LEDs will indicated the status at each stage of programming
To see more about the results of your programming (debug messages from avrdude), you will need to access some files on your raspi. During each cycle of programming, the output from avrdude is saved to some text files that live within /home/pi.
/home/pi/fuse_results.txt
/home/pi/flash_results.txt
/home/pi/SERIAL_UPLOAD/serial_upload_results.txt -- Note that this will only be updated if you did any serial uploading