To function properly, the three key elements of an adaptive optics system must be properly registered. At the Starfire Optical Range (SOR) of the Air Force Phillips Lab we have developed a set techniques which align the Lenslet array to the WFS camera, and register the DM to the Lenslet array. The former uses the spot centroids to factor misalignment into X,Y translation, magnification, and rotation. The latter process, using an insight from Jim Spinheme of RTS, takes advantage of the mirror mode called "waffle." It can generate the same misalignment factors for deformable mirror (DM) misregistration. These two techniques are implemented in the wavefront sensor (WFS) user interface, as a convenient, easy to use tool. Both theory and implementation are presented.