Theme in wp-content but my index.php search theme files in root

I assume you are adding your stylesheets like this in your header:

<link rel="stylesheet" type="text/css" href="https://wordpress.stackexchange.com/questions/285785/css/style.css">

Which won’t work. To construct the path dynamically, you need to use the PHP functions offered for this. Make sure your header has <?php wp_head(); ?> in it, and then enqueue your style in your theme’s functions.php file as follows:

add_action( 'wp_enqueue_scripts', 'enqueue_my_styles' );

function enqueue_my_styles() {
    wp_enqueue_style ( 'style-name', get_template_directory_uri() . '/css/style.css' );
}

This will automatically prepend the theme’s URI to your CSS file, and output it in your theme’s header.