How to setup a popup registeration page in wordpress with function.php

You can add the HTML for the area via wp_footer, include the style with wp_enqueue_style(), and include the javascript to show/hide the popup with wp_enqueue_script().

wpse90382_popup_function() {
    add_action( 'wp_footer', 'wpse90382_popup_html' );
    wp_enqueue_style( 'your_style', get_template_directory_uri() . 'your_stylesheet.css' );
    wp_enqueue_script( 'your_script', get_template_directory_uri() . 'your_javascript.js' );
}
wpse90382_popup_html() {
    ?>
        <div>Your HTML</div>
    <?php
}
if ( some condition )
    wpse90382_popup_function();