How to add iOS & fav icons to the theme?

Hook into wp_head in your functions.php file. 

add_action('wp_head', 'add_your_stuff');
function add_your_stuff() {
    ?>
    <link rel="shortcut icon" href="https://wordpress.stackexchange.com/questions/157869/<?php echo get_stylesheet_directory_uri();?>/favicon.ico" type="image/x-icon" />
    <link rel="apple-touch-icon" href="<?php echo get_stylesheet_directory_uri();?>/apple-touch-icon.png" />
    <link rel="apple-touch-icon" sizes="57x57" href="<?php echo get_stylesheet_directory_uri();?>/apple-touch-icon-57x57.png" />
    <link rel="apple-touch-icon" sizes="72x72" href="<?php echo get_stylesheet_directory_uri();?>/apple-touch-icon-72x72.png" />
    <link rel="apple-touch-icon" sizes="76x76" href="<?php echo get_stylesheet_directory_uri();?>/apple-touch-icon-76x76.png" />
    <link rel="apple-touch-icon" sizes="114x114" href="<?php echo get_stylesheet_directory_uri();?>/apple-touch-icon-114x114.png" />
    <link rel="apple-touch-icon" sizes="120x120" href="<?php echo get_stylesheet_directory_uri();?>/apple-touch-icon-120x120.png" />
    <link rel="apple-touch-icon" sizes="144x144" href="<?php echo get_stylesheet_directory_uri();?>/apple-touch-icon-144x144.png" />
    <link rel="apple-touch-icon" sizes="152x152" href="<?php echo get_stylesheet_directory_uri();?>/apple-touch-icon-152x152.png" />
    <?php
}

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