You could potentially replace the SiteAssist template with your new one, but you will first need to ensure that you have matching editable regions, otherwise the pages in your site will not fit into the new template neatly. If you have a copy of your site or can create one I would suggest doing that first.
You can also use your new template to create a new SiteAssist layout with the preset/layout manager. Just select SiteAssist Pro Layouts in the preset manager and click the new button to begin creating one. There is more info on this feature and support materials that can be found on the SiteAssist Pro support page: