What's the difference?
There are two techniques that you can use to check your email. POP (Post Office Protocol) and IMAP (Internet Message Access Protocol). Each has their benefits and shortcomings. POP downloads all of the messages to your machine where you can access them while IMAP leaves the messages on the server and requires that you have an active Internet connection to read them.
Use POP if ...
You're reading the messages from your primary machine.
You want a copy of the messages on your local machine. This may be useful if you're paying by the minute for your Internet connection. You can download all of your messages and then log off the Internet.
You want to make sure you don't go over your quota on your INBOX.
Use IMAP if ...
You check your mail from more than one location and want your all of your mail to be available from all locations
Have an Internet connection where you're not paying long distance charges to connect. IMAP requires that you be connected to the Internet to read your messages.
You're not worried about going over the quota on your INBOX
What about SMTP?
SMTP stands for Simple Mail Transport Protocol and is used to send messages. POP and IMAP are used to receive messages. For outgoing mail, your only choice is SMTP, but you have your choice for incoming messages.