The behavior you are describing is not typical Dreamweaver template behavior. You should not have to open up the dependent pages individually to get the template to update them. You should only have to update the template file and have all of the dependent files updated based on the changes made to the template. When you make a change and save the template you will be prompted to update the dependent pages. You will have the option to not update these pages as well. It is possible that you choose to not update the pages and that choice was persistent so you are not being prompted to update the pages any more.
This template updating functionality is not a product of the SiteAssist Professional tool but is built into DW. Making updates directly to the template file does not change any of the SiteAssist specific settings.