Settings available for both POP and IMAP accounts:
Delete mail: if ticked, messages will be deleted from the server when they are deleted from your Trash folder.
Skip large emails: if ticked, large messages will not be automatically downloaded. You can retrieve the large messages by choosing Get this mail when viewing a message that has not been fully downloaded.
Synchronize with server: if ticked, the Messages application remembers the list of mails on the POP server. Most users should have this option ticked.
Base folder: if you wish to see only those messages within a particular IMAP folder, enter it here.