Up to V3.2 you would manually type in the MAC address when equipping a phone in session manager.
V4 onwards you could add the IP Phone license and tell it to register via PIN number, the phone would boot, download it's firmware then ask for a PIN, as you have found.
The PIN is programmed under System / Devices and Feature Codes / Endpoint (or Phone) related information.
It makes it so much easier using the PIN number, better than typing in 100s of MAC addresses!
You have to type in the extn number you want the phone to be then PIN number and then press the blue Superkey.
Or is it PIN then Extn number?? One of the ways definitely works