Control Prefabs that come with NGUI's examples are on the 2D UI layer, so they always try to parent themselves underneath the appropriate game object when you drag them into the scene. They shouldn't be creating any other extra UI roots however. I just did a quick test on my end -- created a 2D UI, then a 3D UI, and dragging in prefabs from the Prefab Toolbar automatically adds them to the 2D UI's hierarchy, as expected.