IMAP or POP3, this is the question

IMAP does much of its work on the server, where your email is usually kept.
POP3 does the work on your PC, since your mail is downloaded to your PC from and off the POP servers.

    993 is the port assigned to secure IMAP over SSL

You can view folders with IMAP in X-notifier.
But you can't with POP3.

Let talk about IMAP...
You saw new email on X-N (IMAP), did not click on X-N
and go ahead open in Thunderbird.
You check email in Thunderbird,
X-N will change the value go up (if you click 'unread')
and go down (read the email) accord your checking IMAP email in Thunderbird.

Let talk about POP3
You saw new email on X-N (POP3), did not click on X-N
and go ahead open in Thunderbird.
You check email in Thunderbird,
X-N will NOT change the value go up (if you click 'unread')
and go down (read the email) accord your checking POP3 email in Thunderbird.
You need to click POP3 on X-N to "reset to zero".