add_action( 'woocommerce_before_checkout_form', 'custom_payment_overlay' );
function custom_payment_overlay(){
	echo sprintf('<div class="custom-payment-popup"><div class="wpt-payment-overlay"></div><div class="wpt-payment-message">%s</div></div>',
		'We are processing your payment. Please hold on and do not refresh your browser.'
	);
}