How does the API handle if a customer orders multiple magazines in a single order?

You should do separate Subscribe calls for each subscription, there is no support for bundling multiple orders besides a batch file API and we prefer you use the restful API for immediate responsiveness. That way you can put the issue up in an Iframe, for example.

The entitlement token will be different for each subscription: it represents immediate access to the current active issue for that subscribed title.