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.