How to upgrade Xcode 4 to 4.1?
You need to install XCode 4.1 from the app store, which will replace XCode 4.0 with 4.1.

When updating XCode to 4.1 you will get a message to quit iTunes to continue the installation. The installation is actually waiting for iTunesHelper process to be terminated. You can terminate the iTunesHelper process using activity monitor.

On my Mac the upgrade to XCode 4.1 failed. So I needed to uninstall XCode 4.0 first.