you can set the main view, the default layout, layouts dir and partial dir
$view->setLayoutsDir('/path/to/layouts/');
$view->setPartialsDir( '/path/to/partials/');
$view->setMainView('/path/to/default/view'); // notice the missing trailing slash
$view->setLayout('defaultLayoutName');
If absolute paths don't work, try relative ones. Absolute paths might not work when your path is outside the module.