Having template files in different folders has nothing to do with styles not working.
View page source and make sure the right stylesheet is loaded. If its loaded, then double check if there is any other rules thats overriding your needed rules for specific class. Try adding !important to the css definitions and see if it works.
This is how you should add stylesheets to frontend output, you need to add this code in your functions.php inside your active theme.
function my_custom_css() {
wp_enqueue_style( 'style-name', get_stylesheet_uri() );
}
add_action( 'wp_enqueue_scripts', 'my_custom_css' );
Hope this helps 🙂
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