Mailwasher will list all messages on the server. If you have configured your email program to leave messages on the server, it [the mail program] will track which ones have already been retrieved and only get the new ones. Mailwasher, however, will continue to display all messages on the server.
"Also how do I ensure that on loading WLM, that emails are NOT automatically downloaded as I would rather they wait for Mailwasher?"
If using POP3, your email program shouldn't be configured to retrieve messages automatically. Mailwasher should check periodically for new messages, you should look to see which messages you want to keep and which to get rid of and only then do you get your email program to download the messages you want.
However, if you're using IMAP, where the program continuously synchronises with the mail server, you need to wait until you've finished processing messages in Mailwasher before launching your email program.