The micro controller is an Atmega328p so it can be programmed using the Arduino IDE. The method discussed here uses an Arduino Mega 1280 as an ISP. First, connect the Arduino Mega to a six pin ISP connector. This example uses a pogo pin adapter from Sparkfun. Six connections must be made to the Arduino Mega from the pogo pin adapter. Reset connects to pin 53. MOSI connects to 51. MISO connects to 50. SCK connects to 52. Vcc connects to +5 and ground connects to ground on the Arduino board. The ArduinoISP example sketch comes preloaded with version 1.06 of the Arduino IDE. The comments of this sketch also list these connections.
After connecting the Mega to the pogo pin adapter the pins are pressed onto the board. To use the Arduino Mega as an ISP in the IDE select the “Arduino as ISP” programmer under “Tools/Programmer.”
From this point you can directly upload you code with the “Upload using programmer” under “File.” Control-shift-u performs the same command. Another option is to load an Arduino bootloader. The PCB for this project runs at 8MHz and 3.3V so choosing the “Arduino Pro or Pro Mini (3.3V, 8MHz) w/Atmega328” board under the “Tools/Board” menu will select the correct bootloader. To burn the bootloader use “Burn bootloader” in the “Tools” menu.