With the Apple FAQ, I know I can not deploy on the app store if I am enrolled in an iOS Developer Enterprise Program (https://developer.apple.com/support/ios/enterprise.html). I understand that I have to create a standard iOS Developer Program to do that.
The point I don’t understand is how to manage it on my xcode?
As a developer, how can I be part of an enterprise program and a standard program? Because I want to continue to develop application for the in-house, but I also want to be able to deploy some other applications on the app store.
The provisioning profile you select when building an release version of you app is what identifiers if the app is an Ad-Hoc, Enterprise or appstore version.
You can therefor easily create targets for each type.