The protocol options are just different ways of using the email.
IMAP means it is like you are connecting to the server and any changes you make in your client are instant on the server. For example if you are on your cell phone checking your email if you delete the email it will also delete it on the server.
POP3 is just where you download the messages. So if you were on your phone and deleted the message it would only delete it on your phone.
