Putting any file here which has the same name as a template file in the root templates directory will make this file be used by Tiki instead of the file in the root templates directory.
This helps you customise your templates without conflicts with the files you get from Tiki on upgrades.
If you want to customize templates for a single theme or theme option, do it in themes/themename/templates/ or themes/themename/options/optionname/templates/
After modifications in template files, you need to clear caches from Tiki or in command line:
php console.php cache:clear