1. Navigate to the Client Portal Administration window from the top right drop down menu
2. Click on Manage Portal to the right of the Client Portal you want to customize
3. Click on Actions then select Customize Portal. 
4. This will provide you a list of folders and files that are linked to your portal
5. Navigate to the site logo folder, delete the default logo, then upload your own logo. This will update the logo on your client portal
6. Navigate to the other folders and update the items as needed to make changes to your client portal