1) Open Thunderbird
2) Click on "Tools" in the menu bar, and then "Account Settings"
3) The window below will then appear. In the Account Settings window click on "Add Account"
4) The window below will then appear. Select "Email Account" and click "Continue"
5) Put in "Your Name" (the name that you want to appear in your outgoing emails) and enter in your "Email Address"
6)On the Server Information screen choose POP. Enter your incoming server. It'll be mail.yourdomain.com (replace yourdomain.com with your actual domain name.) If you have an Outgoing box enter the same thing.
You can choose to have the Global Inbox be where your emails get sent to, but in my opinion it's better to use the inbox for each mail account.
7)On the User Names screen enter your email address as the username for both the incoming and outgoing server. If you already have an email account setup with Thunderbird you'll only see a box for the incoming server.
8)The Account Name screen is where you can give a descriptive name for the email account.
9)You're almost done. Back on the Account Settings screen go to the Out Going Server screen.
Make sure that "Use Name and Password" is checked.
You're now finished.