IMAP email access coordinates between the server and your mail application. Messages that have been read/deleted/replied to will show up as such, both on the server and in the mail application.
POP3 does not coordinate with the server. Messages marked as read/deleted/replied to in the mail application will not show up as such on the server. This means that future mail downloads with POP3 will show all messages as unread. Outgoing mail is sent using SMTP.
We recommend using POP3 over SSL/TLS or IMAP over SSL/TLS since they provide increased security for your interactions with the remote mail server.