A great use example of why you would want to set up an exclusion folder is if you previously had work mail forwarded to your personal account. In this example we'll use this case: Work Email is being forwarded to your personal gmail account. The Goal is to move all work Gmail to a Company owned Google Apps Account.
1. In the search bar of your personal Gmail account, enter the following search phrase to:email@example.com where firstname.lastname@example.org is your personal email address..
2. Click the search dropdown (arrow by search button) - this brings up the Filter Dialog Box.
3. Check the Apply the Label: - Choose to create a new Label, call it Exclude.
4. Towards the bottom of the dialog, select Also apply filter to matching conversations.
5. Click Create Filter
That's all you need to do. Any items in this folder/label will be ignored by the Google Apps Migration Tool. Some notes: