Mac App Store: download but don't install
The Xcode you download from the app store is just an installer, it's not the actual Xcode; downloading it will not compromise your current installation of Xcode (that is if you do not open it).

P.S. The Xcode from the AppStore (4.1) runs only on Lion. For Xcode on Snow Leopard download it from the developer's website(Xcode 3.6).