Custom CSS is overwritten by WordPress?

I do assume you have functions.php file in your theme directory after that you can add following code :

/*Section for enqueuing styles and scripts*/
    function keyword_theme_styles_and_scripts(){
        /* Styles Below */
        wp_enqueue_style('bootstrap-min-css', 'https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css');

        wp_enqueue_style('video-js-min-css', get_template_directory_uri().'/assets/css/video-js.min.css');

        wp_enqueue_style('google-fonts', 'https://fonts.googleapis.com/css?family=Open+Sans:300italic,400italic,600italic,700italic,800italic,400,300,600,700,800');

        wp_enqueue_style('font-awesome-min-css', get_template_directory_uri().'/assets/font-awesome/css/font-awesome.min.css');

        wp_enqueue_style('magnific-popup-css', get_template_directory_uri().'/assets/css/magnific-popup.css');

        wp_enqueue_style('animate-min-css', get_template_directory_uri().'/assets/css/animate.min.css');

        wp_enqueue_style('device-mockups-min-css', get_template_directory_uri().'/assets/device-mockups/device-mockups.min.css');

        wp_enqueue_style('main-css', get_template_directory_uri().'/style.css');

        /*  Scripts Below */

        wp_enqueue_script('jquery-min-js', get_template_directory_uri().'/assets/js/jquery.min.js', array(), '', true);

        wp_enqueue_script('video-min-js', get_template_directory_uri().'/assets/js/video.min.js', array('jquery-min-js'), '', true);

        wp_enqueue_script('bootstrap-min-js', 'https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js', array('jquery'), '', true);

        //wp_enqueue_script('bootstrap-min-js', get_template_directory_uri().'assets/bootstrap/js/bootstrap.min.js', array('jquery-min-js'), '', true);

        wp_enqueue_script('jquery-easing-min-js', 'https://cdnjs.cloudflare.com/ajax/libs/jquery-easing/1.3/jquery.easing.min.js', array('jquery-min-js'), '', true);

        wp_enqueue_script('scrollreveal-min-js', get_template_directory_uri().'/assets/js/scrollreveal.min.js', array('jquery-min-js'), '',true);

        wp_enqueue_script('jquery-magnific-popup-min-js', get_template_directory_uri().'/assets/js/jquery.magnific-popup.min.js',array('jquery-min-js'), '', true);

        wp_enqueue_script('svg-injector-min-js', get_template_directory_uri().'/assets/js/svg-injector.min.js', array('jquery-min-js'), '', true);

        wp_enqueue_script('wow-min-js', get_template_directory_uri().'/assets/js/wow.min.js', array('jquery-min-js'), '', true);

        wp_enqueue_script('index-min-js', get_template_directory_uri().'/assets/js/index.min.js', array('jquery-min-js'), '', true);

    }
    add_action('wp_enqueue_scripts', 'keyword_theme_styles_and_scripts');

Remember to enqueue your custom styles and scripts at the bottom of the queue.

and order of the scripts ans styles matters as well so enqueue in proper order.

I hope it helps.

Good Luck!!!

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