Phone is the actual device ( like the 7821, 9971, 8841 etc ) , Extension is the directory number associated with that device ( like 1001, 2000 etc ) and User is the account that is used to login into the phone or associate to various services and features.
You can check the CME admin guide if you really want to dive into the details of all these
http://www.cisco.com/c/en/us/td/docs/voice_ip_comm/cucme/admin/configuration/manual/cmeadm.html
Manish
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