You can approach your problem in two separate ways.
1 - Routes : Did you setup a different route for adding an issue to each magazine?
In your controller you can do something like:
if ($form->isValid()) {
...
$magazine = $this->getManager()
->getRepository('AcmeBundle:Magazine')
->findOneBy($magazineId); // /{magazineId}/issue/new
...
$issue->setMagazine($magazine);
$em->persist($issue);
...
}
Also you can read the docs for route parameters.
2 - Single Form: If you add a new issue in the same route /issue/new
When adding your Issue fields to the $formBuilder add a dropdown list to asign the Magazine
$builder->add('magazine', 'entity', array(
'class' => 'BundleNamespace:Magazine',
//If your class does not have a __toString() method add below
'property' => 'title',
));