Include different scripts and styles for two separate custom headers?

Check whatever conditions you want to enqueue specific scripts on within your enqueue function.

function wpd_enqueue_scripts() {
    if( is_user_logged_in() ){
        wp_enqueue_script( 'script-name', get_template_directory_uri() . '/js/logged-in.js', array(), '1.0.0', true );
    } else {
        wp_enqueue_script( 'script-name', get_template_directory_uri() . '/js/not-logged-in.js', array(), '1.0.0', true );
    }
}
add_action( 'wp_enqueue_scripts', 'wpd_enqueue_scripts' );