We recently enrolled in the iOS Enterprise Developer Program to be able to use in-house distribution, which significantly simplifies the deployment of the apps inside our company which is fairly big. Before joining we have thoroughly read the program documentation and we were aware that the new account would live completely separated from the standard account we use for the AppStore submissions.
What I'm unsure about is now what would be the best way to organize the two accounts in the developer portals. I'm mostly concerned with the bundle identifier since I'll be dealing with two different bundle ids inside Xcode for each application. All of our apps use iCloud and Push notifications so wildcard is not an option.
How do you organize this inside Xcode? Do you create two different targets or are you able to manage this with a new Project Configuration? What about iCloud entitlements?
EDIT
Just as an update I wanted to make clear that we're looking for the best solution to build an app for both In-House distribution and for AppStore submission.
EDIT2
Given that the enterprise program does not grant you access to iTunesConnect, where test users and product ids can be setup, is there really no way to test InApp purchases?