The Device Programming dialog in Atmel Studio 6 is modal, which means you must close it after you are done programming in order to go back to editing your source code. It takes 4 clicks to open up the dialog and initiate the programming process again. This section describes a different method for programming that will allow you to compile and program simply by pressing F5.
First, in the View menu, select “Available Atmel Tools”. This will bring up the “Available Tools” window. Make sure that there is one and only one STK500 in the list and make sure that the COM port number matches the COM port number of the Pololu USB AVR Programmer Programming Port, which is displayed in the Device Manager. If there are multiple STK500 entries, right click on them and select “Remove” to remove the extra entries. You will only have to do this once.
Next, open the project properties window by opening the Project menu and selecting “Properties…”. In the Tool tab, select STK500 as the debugger/programmer, and select ISP as the interface. You will only have to do this once per project. You can also set the ISP Clock speed here but please note that the frequencies displayed in Atmel Studio are not correct when you are using the Pololu USB AVR programmer (see Section 3.e for the correspondence). It is a good idea to set the frequency to something between 80 and 90 kHz (which will result in 200 kHz on the Pololu AVR Programmer) at first and to try increasing it later once F5 programming is working.
Finally, you should be able to press F5 to build your project and program the resulting HEX file onto your AVR! Alternatively you can program by selecting either “Continue” or “Start Without Debugging” from the Debug menu.