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. Please see this article for more Gmail specific information.
The whole point of SaneBox is to get unimportant emails out of your way so that you can deal with your important ones now. We take all of those unimportant emails and put them into SaneLater so that can either archive or delete them when you have a free moment.
Most people that rely on their Inbox tend to feel overwhelmed by the amount of emails in their Inbox. We help you by separating the important from the unimportant and increasing your productivity levels each day.
We have a great webinar that will help explain this concept: