I think the easiest way would be to skip the DIC part and simply instantinate the AcmeManager with the EM passed in the constructor.
The other way would be getting it from the DIC as you currently do, and setting AcmeManager::$em with reflection. Something like this:
$acmeManager = $this->getModule('Symfony2')->container->get('acme_manager');
$class = new \ReflectionClass('\Acme\AcmeBundle\Manager\AcmeManager');
$property = $reflection->getProperty('em');
$property->setAccessible(true);
$property->setValue($acmeManager, $mockedEntityManager);