How POP Works
POP (Post Office Protocol) is the older of the two methods for mail retrieval. In the most basic sense, POP simply grabs emails from your server and downloads them to your email client.
Also, junk mail may be routed into a Spam Folder which is accessible only to IMAP connections. Simply put: If you're using POP, you may not be aware that there are potentially thousands of messages being put into an unchecked spam folder. If you decide to use POP, you can still view these messages using the webmail client for your service. Please see this article for more information on webmail: Using Webmail.
How IMAP Works
IMAP is the preferred method of connecting to your email server. It simply displays the contents of your mailbox as they appear on your server. Also, by default, spam folders are configured to be IMAP-Only, meaning you will need to use an IMAP connection in order to view and delete messages. We recommend using an IMAP connection to both keep an eye on your Spam folder, and to make sure you don't download email from your server that you would like to read elsewhere.