The navigation that is present on each page should directly reflect the navigation that is present in the template file. If you make your changes to this template file then you should not have to update each page individually. After you make the changes in your Site Assist template file and save you will be prompted to update all of the files that are based on that template, if you choose to update the other pages they will all be set just like the template page.
If you want to change the structure of the site that is created with SiteAssist then you should alter the navigation in this template file first, then move the pages into their new locations that match the navigation updates you have made.
