Note: You can use the mkII programmer with the 2x5 header that some people originally soldered on their $50 robot board, if they buy or make an adapter:
http://www.sparkfun.com/commerce/product_info.php?products_id=9046
http://www.sparkfun.com/commerce/product_info.php?products_id=8508
http://www.sparkfun.com/commerce/product_info.php?products_id=8535
The AVR MKII Programmer , otherwise known as the AVR ISP2 Programmer is a great tool for programming your AVR microcontroller from your computer. Its rather cheap for a tool of its caliber ( $34 USD) and can be purchased from Digikey - http://jp.digikey.com/scripts/DkSearch/dksus.dll?Detail?name=ATAVRISP2-ND or from Mouser - http://mouser.com/Search/ProductDetail.aspx?qs=sGAEpiMZZMv256HIxPBQcA8%252bsNH3cLLR .

This tutorial will only cover Windows XP users and not Windows Vista users nor Mac nor Linux users. Windows Vista users have reported problems with the AVR MKII, so if you have Vista you have two options : Install XP or Download and Install a Free Virtual Machine that runs Windows XP. This tutorial also assumes that you have AVRstudio installed - http://www.atmel.com/dyn/products/tools_card.asp?tool_id=2725 .
The first step to programming with your AVR microcontroller is to connect your AVR programming connector to the AVR microcontroller . Connect MOSI of the connector to MOSI of the microcontroller, MISO to MISO, VCC to VCC , etc.

Many microcontroller boards already have ISP programming sockets so you can just plug in the ISP connector into that. My Axon and Roboduino already have ISP programming sockets built in.

Once you have your programmer, plug the programmer into your computer's USB Port.
A few seconds after you plug it in you should see a windows pop up which asks if you want to locate
drivers automatically. Choose to install software automatically and wait a few minutes until it installs.
Now that your drivers are installed just open up your AVRstudio project. Press build to Build your current project.

Turn on your microcontroller board, the light inside the AVR programmer should turn green. Then click the Programmer Button in the toolbar -

A window should pop up. Select AVR MKII Programmer and select USB.

Click "Connect" and now another window should pop up.

Now verify that the device selected is indeed your device. Click the "Settings" button right above ISP Frequency, and set your ISP frequency to 125 kHz.
Now select the Program tab and verify that the file in the Input Hex File textbox is indeed your hex file that was generated from your code.

Press the Program button directly underneath the Input Hex File .Your microcontroller should program now.
Now if this is your first time programming with your AVR MKII programmer , chances are that its not working properly.
Servos Jittering While Programming: This happens sometimes because the programmer applies some power to pins while its programming. Don't worry about it.
Debugging Techniques
Common Problems and Solutions