domain.com/website1/store1
domain.com/website1/store2

domain.com/website2/store1
domain.com/website2/store2

$mageFilename = MAGENTO_ROOT . '/app/Mage.php';

$mageFilename =  '../app/Mage.php';

/* Store or website code */
$mageRunCode = isset($_SERVER['MAGE_RUN_CODE']) ? $_SERVER['MAGE_RUN_CODE'] : '';

/* Run store or run website */
$mageRunType = isset($_SERVER['MAGE_RUN_TYPE']) ? $_SERVER['MAGE_RUN_TYPE'] : 'store';

Mage::run($mageRunCode, $mageRunType);

Mage::run('website1_code_goes_here', 'website');

$mageFilename = MAGENTO_ROOT . '/app/Mage.php';

$mageFilename = '../../app/Mage.php';

/* Store or website code */
$mageRunCode = isset($_SERVER['MAGE_RUN_CODE']) ? $_SERVER['MAGE_RUN_CODE'] : '';

/* Run store or run website */
$mageRunType = isset($_SERVER['MAGE_RUN_TYPE']) ? $_SERVER['MAGE_RUN_TYPE'] : 'store';

Mage::run($mageRunCode, $mageRunType);

Mage::run('store1_id_goes_here', 'store');

require realpath(__DIR__) . '/../app/bootstrap.php';
$params = $_SERVER;
$params[MagentoStoreModelStoreManager::PARAM_RUN_CODE] = 'web2_website';
$params[MagentoStoreModelStoreManager::PARAM_RUN_TYPE] = 'website';
$bootstrap = MagentoFrameworkAppBootstrap::create(BP, $params);
$app = $bootstrap->createApplication('MagentoFrameworkAppHttp');
$bootstrap->run($app);