The name that appears under your application in the app store is set in iTunes connect. You can't set it per app... the name is a one time thing - you can't change this, unless you buy a new developer account!
You set the name that displays under the application icon on the home screen of your iphone in info.plist. This is the Bundle display name. The application title in the app store is set in itunes connect (and the version number - although you do have to specify a version number in XCode as well, and if the version number differs from XCode to ITunes connect - I've heard - your app will be rejected).
Just go through the process (like everyone else) and you'll understand.