POP (Post Office Protocol) and IMAP (Internet Message Access Protocol) are both means to retreive emails from a remote email server. Which one you use depends on what you need to be able to do with your email. The primary differences between POP and IMAP involve what you can do on the email server.
POP
POP was designed with dial-up connections in mind. You can log on to your email, download all of your messages to your computer and then disconnect. The advantage is that you don't have to stay online to read or organize your emails. By default POP is set to delete messages from the server when you copy them to your computer, although there is an option to leave a copy on the server. Unless you select this option, you can only view your emails from one location. However, deleting messages from the server means that your email storage is not limited by the email server's storage limits. This means that you can save as many emails as your personal computer can hold. The only folder on your email server when using POP is the Inbox. You can't create other folders for sorting emails on the server, only on your local computer, so these folders can only be accessed on that computer. In essence, the control center for working with your emails when using POP is your computer not the email server. The bottom line is that you should use POP for any email account that you access from only one computer or any account that might exceed your email server's storage limits.
IMAP
IMAP was designed as an alternative to POP. Instead of downloading messages to your computer, emails are saved on the server and you see only the header of the message on your computer. This allows you to access the same emails from different locations. You can also create different folders on the email server, allowing you to organize your emails on the server, then access those folders from multiple locations. Because your messages are stored on the email server and not your personal computer, you do have to manage your storage space. When your email server/account gets full, incoming emails will be returned to the sender. You can download and delete messages from the server (like with POP), but the process is not as straightforward. The control center for working with your emails when using IMAP is the email server, not any one computer. The bottom line is that you should use IMAP for any email account that you access from multiple computers.