Here are your options.
1) Texture the inside of a dome in your 3D scene with an HDRI sky and render.
2) Render a traking pass and use it to track in the sky.
3) Render a UV map and use it to warp the sky in shake with the following node:
CODE
DisplaceX1 = DisplaceX(0, 0, 1, width*r, height*g, 0, xDelta);
4) Output your camera information as a .MA file and input it into the multiplane node.
5) Hand track the sky using move2D or Move3D nodes
6) Do a 2 point track from the render, play with the paralax untill you have the movement looking realistic
I suggest that you read "the art and science of digital compositing" by ron brinkman for an understanding of some of these processes.