Uploading a hex file using AVR Studio:
* build the code using the Arduino IDE
* retrieve the hex file from \
* open AVR Studio and the programmer tool
* attach the programmer to ISP pins, with pin 1 closest to the SD card slot
* set clock rate to 500khz
* in the 'memory' tab select the hex file and program
If you get timeouts it could indicate that the clock speed set on the programmer is much lower than it should be. I encountered this issue, and empirically arrived at the 500khz as the fastest I could communicate with the printrboard (rev D).