As you wrote yourself the Axis tool in the timeline is designed to affect only 1 layer in your timeline. To work with multiple layers and create axis that can control multiple layers you will have to use the Action tool. But the good thing is your work you have done in the timeline using the axis tool can easily be converted into the Action tool. Select your layers in the timeline and from the FX ribbon click the Create ConnectFX option. Make sure you have the option “Generate Composite” enabled be foe you click the ConnectFX button and Smoke will create the Action node with your selected layers converted into layers. Plus any transformation you did in the Axis tool also converted. Then in the Action schematic view you can add a new axis node and connect it to the other layers so it will be a parent to multiple layers and you can scale, rotate and change position to all layers that are the child of the parent Axis.
Autodesk Smoke Technical Marketing Manager