Once the 3D option is enabled on a layer, the Rotate tool will work as a 3D Rotate tool on that layer. This tool is able to rotate elements on all three axes.
You can click on the direction ellipses to rotate your layer on one axis only. If you click anywhere else, the layer rotates freely on two axes at once. Once the ellipse is selected, it will turn pink.
NOTE If you move the layers in the Perspective view, it may be difficult to control the motion since you may not have the optimum point of view on your stage to understand the setup. In this case, it is best to use the direction ellipses.