The first step should be loading the Arduino application on your computer and running the blink app. This is the "Hello World" for Arduinos and should tell you if your micro controller is working. See the picture to find where it is.
After running the blink sketch then install Node version 4.2.1 if you haven't already. You can find it here https://nodejs.org/en/blog/release/v4.2.1/ . Then install yeoman at by doing
npm install -g yo and johnny-five generator by executing in a terminal
npm install -g generator-johnny-five .
Finally create the scaffolding to your project doing
cd yo johnny-five
Then follow the generator and do node index.js