- You can change your iTunes App Name each time a new binary is submitted.
- You can change your .app bundle name each time you upload a new binary (this is changed in the info.plist).
- If the app is already in the App Store, you'll have to submit an update to change the app name(s).
In order to get the two to match, you need to upload a new compressed binary with an app name that at least resembles the iTunes App Name. Since you can only show a small amount of the name on the Springboard (app launch view on the device), a lot of people abbreviate or shorten the name.
As an example, say you have an app called "My Brand New App" in iTunes (since this name can be longer). Well, you'd wanna shorten that name or abbreviate it in the .app bundle to be something like "New App" or similar so the entire name would fit under the app icon without being truncated by the OS.