IK handles need to be parented to a transform node to work correctly.

Create a locator, or curve, any thing you want to use as a controller for your IK handle and snap it to the ik handle.
Freeze the transforms on your control object and parent the IKhandle to the controller.

This will ensure that when you key the rotates of joints further down the rig that the ik chains will point towards the handle. To animate the IK just transform and key your new controller. Its also wise to create pole vector constrains which will control the plane of the ik solve.

To do this again just create any transform to use as your controller, move it into position, freeze transforms then select your controller, shift select the ik handle and contrain> pole vector constrain.