To invoice an order you need to have in hands the number of the fiscal note to send it on request.
// ...
/** @var \SkyHub\Api\Handler\Request\Sales\OrderHandler $requestHandler */
$requestHandler = $api->order();
$nfKey = '99999999999999999999999999999999999999999999';
/** @var SkyHub\Api\Handler\Response\HandlerInterface $response */
$response = $requestHandler->invoice($orderId, $nfKey);
// ...For more information, access the official_documentation.