The Pi 3 should work great with EspruinoHub, so no worries there. I think next step would be to check out that status page.
I am not sure if I have to pair the Puck to the Pi or to the PC.
The Puck needs pairing with the PC to work with the standalone IDE, but it doesn't need pairing with the Pi at all. Only thing to watch out for is you can only have one connection at a time - so if you're connected to the PC then the Pi won't be able to see the Puck... But that wouldn't have been an issue when you first tried.
Espruino is a JavaScript interpreter for low-power Microcontrollers. This site is both a support community for Espruino and a place to share what you are working on.
The Pi 3 should work great with EspruinoHub, so no worries there. I think next step would be to check out that status page.
The Puck needs pairing with the PC to work with the standalone IDE, but it doesn't need pairing with the Pi at all. Only thing to watch out for is you can only have one connection at a time - so if you're connected to the PC then the Pi won't be able to see the Puck... But that wouldn't have been an issue when you first tried.