Javascript Reference

That's correct, yes. There's some good info on where to look here, after the list of tutorials: http://www.espruino.com/Puck.js+Quick+Start#what-now-

Basically, you have:

• Puck Object - for Puck.js specific functionality
  
• NRF Object - for nRF52 Bluetooth functionality
  
• Global Functions and E Object - for built-in Espruino functionality
  
  

How to use the onboard peripherals is documented here as well: http://www.espruino.com/Puck.js#on-board-peripherals