I would not recommend using the Auto Configure for your email accounts offered in cPanel. This has been known to incorrectly setup the email account in your email client.
If you would like to setup an email account in Thunderbird, you would need to click 'Tools' > 'Account Settings...'. On the window that comes up, you will see a button that says "Add Account". Click here to setup your new email account. You would need to use the 'Email account' option to setup email accounts.
Mail settings should be as follows:
smtp server: yourdomain.com (replace 'yourdomain' with the actual name of your domain)
pop3/imap server: yourdomain.com (replace 'yourdomain' with the actual name of your domain)
pop3 username:
youremailaccount@yourdomain.com (if you have created your own email account in your cpanel) or your cpanel username (does not require the @yourdomain.com)
smtp username: same as your pop3 username.
Please note that smtp authentication must be used on our servers.
Secure Password Authentication (SPA) should not be used.
If your email client has problems using the @ symbol for the username then you can use :, + or % sign instead.
Hope this helps.