You need to make sure EE knows where your templates are located.
Sign into your control panel and navigate to: Design -> Templates -> Global Preferences
Change the settings for Save Templates as Files
to Yes
and then change Server path to site's templates
to the location of the template files you added.
Usually I would create a new folder: /themes/site_themes/myNewTheme
, then templates will be stored in /themes/site_themes/myNewTheme/default_site/
After changing the settings navigate to Design -> Templates -> Synchronise Templates, select all the templates and click submit.
Hopefully that should do the trick :)