Problem: Unity 4.6 and 5.0 installer wants to install into the /Applications "Unity" folder.
I've found it's super easy to keep both my Unity 4.6 and my Unity 5.0 both installed AND updated by understanding the install process and setting up your folders.
Unity 4.6.p1 is named "Unity 4.6"
Unity 5.0.b14 is named "Unity 5.0"
I also replace the Unity 5 beta icons to when they are running and on my dock I can easily tell which version is which.
To maintain: Download the updated Unity and run the installer. Once complete, rename your original folder (like "Unity 5.0.b13) and then rename the "Unity" folder to match the version you downloaded.