You can and should archive, delete, or file any mail you find in a Sane folder once you are done with it. Remember, the goal is to have an Inbox of zero, and removing the email once you are done with it will help you get there.
To archive using Gmail, click Remove label (or if you use Gmail short cuts click the y button). You can use this method for SaneLater, SaneNews, SaneBulk, and SaneNotSpam.
In the case of SaneTop emails, there are two Sane labels: SaneTop and Inbox. You only need to remove one. Once we see that, we will remove the other for you. Note that this may take a few seconds to work due to IMAP notification delays.