In my experience the Polycoms can only do BLF for one registration, and they default to the primary registration. You can change it to the secondary registration and do BLF for extensions on the server of the secondary registration. I'm not sure how you would set it up in EndPoint Manager (we use our own provisioning), but if you look in the config file for that phone and find the section. In there, you should have a line that says:
attendant.reg="1"
If you change the "1" to "2" then the Polycom will use the server for the second registration for BLF subscriptions.