First of all, connect the usb cable on your Nectop (or computer if you don't have a Nectop).
Then, open the Code Editor, open the examples folder and open a terminal.
Now, you just have to type :
nectar arduino-led.js --target arduino-mega2560 --env arduino --flash /dev/ttyACM0
ttyACM0 represents the place where our IOT board is cabled.
NectarJS will understand that you are targetting an Arduino Mega 2560 with the Arduino env.*
Once compiled, you should see the led blinking.
Easy, isn't it ?