You can't distribute apps on the App store with an iOS Developer Enterprise Program account (see the Enterprise account FAQ).
If I am enrolled in the iOS Developer Enterprise Program, can I distribute my apps on the App Store?
No. The ability to distribute apps on the App Store is only available to developers enrolled in the standard iOS Developer Program. The iOS Developer Enterprise Program only allows you to distribute your apps to employees or members of your organization through Ad Hoc distribution.
If your company is enrolled in the iOS Developer Enterprise Program but would also like to distribute your app(s) to customers on the App Store, you will need to enroll in the iOS Developer Program.
Only iOS Developer Program can create provisioning profiles which can be used to submit apps to the App store.
You should sign up for a iOS Developer Program account and then you will have the following option when creating a provisioning profile.
If you want to distribute your application (make sure you don't break the license agreement - §2.6 No Other Permitted Uses) you should use the middle option when creating an IPA in Xcode.
The offical Apple process for deployment and distribution can be found here (This is probably the better document to look at on that page).