The recommended method is to use a master controller as mentioned above. Make sure all of the layers in your rig are ultimately parented to the master controller. But, for use in 3D you should also parent the limb layer to the master controller. Enable the 3D switch for every layer in your character, including the limb layer(s), controllers and master controller. If you want to move your character in the Z plane, alter the Z Position value of the master controller only (we recommend separating dimensions on the master layer to make this easier). If everything is parented correctly, the entire character will move in Z space and still function normally.