Our math is pretty simple All = Incoming + Later + Done. Some of our users use mail in a classic way, operating on your “All” inbox, using flags, or mark as read / unread to track important emails. All and Unread may help you use this style.
Others prefer a zero inbox approach, where initially your incoming mail is all of your mail. As you process your email, you Get things Done (by marking email Done or handling it with reply depending on your settings), delete them, archive as reference, or defer it for Later. This is where Incoming | Later | Done | Unread come handy.
By default this Filter is set to All. You can use Grid Menu | Settings | Global Settings | Default Inbox to preset it (e.g. to Incoming).