The portal layouts page is used to assign a template header, body and footer to each page in the portal. Only one template can be assigned to each section. If different looks are required for the same page in different portals the template editor should be used to define multiple templates under the same template name.
To assign your template click edit against the corresponding page.
Then select from the drop downs the template to assign to the three page sections (header, body, Footer).
Once selected click save.