I never move anything out of the library in case of library updates. I keep a folder on the desktop, and as I use or download ensembles, I save them in the folder under a hierarchal structure such as Reaktor/Drums/Electronic/Beat Machine or Reaktor/Synth/Modular/Sample Mangler.
Also, use the Service Center to download updates, but don't let it do the actual installation. Do the install manually. the service center has a tendency to install things in the wrong areas, especially plugin updates. Installing manually, I've never had a problem.