First of all, don’t forget to ask your sysadmin to setup autodiscover, as it will make the process of setting up Thunderbird much easier.
Click on Tools -> Account Settings -> Account Actions -> Add Mail Account.
If your menus on the top are hidden, click on the ALT key to show them, or access Account Settings by clicking on the radiator icon, on the top right of the interface, then Options -> Account Setting -> Account Actions -> Add Mail Account.
Enter the user’s full name, e-mail address and password:
Click on Continue. Thunderbird will automatically find the proper server names.
Click on Create Account
Note: that Thunderbird will automatically setup the account as IMAP. If you want to set up the account as POP, you have to setup the account manually. IMAP is recommended, as it´s a protocol made to support several devices accessing one same account, with all folders synced at our server, which also guarantees that our backups will be executed.