I am guessing that you created a site and then replaced it with a template.
Templates, in any field, are used at the beginning. When I fixed my new wall mounted phone the other week a template came in the box. It didn't make the holes from the old phone move to the new positions, I had to use the template as a guide to drill new holes.
With a web site you start with the template, open it in an editor and then type in your content. If you take a blank template and upload it to your hosting it will simply replace any identically named pages that were there already.
