NOTE: You can choose between IMAP and POP3 when configuring your mail client. Definitions are shown below:
IMAP: IMAP email access coordinates between the server and you mail application. Messages that have been read/deleted/replied-to will show as read/deleted/replied-to both on the server and in the mail application.
You can learn more about IMAP through Wikipedia at http://en.wikipedia.org/wiki/Internet_Message_Access_Protocol.POP3: POP3 does not coordinate with the server. Messages marked as read/deleted/replied-to in the mail application will not show as read/deleted/replied-to on the server. This means that future downloads of your inbox or other mailboxes with POP3 will show all messages as unread.
You can learn more about POP3 through Wikipedia at http://en.wikipedia.org/wiki/Post_Office_Protocol.