Tracking motion and stabilizing motion are essentially the same process, only with a different target and result. Use Track Motion to track motion and apply the results to a different layer or effect control point. Use Stabilize Motion to track motion and apply the results to the tracked layer to compensate for that motion (for example, to remove camera shake).
To stabilize a layer, After Effects tracks the motion of a feature in the layer that should be stationary in the frame, and then uses the tracking data to set keyframes to perform the opposite motion. You can stabilize to remove any combination of changes in position, rotation, and scale, while leaving desired motion unaffected. For example, if the camera is panning, deselect Position but select Scale and Rotation as the properties to stabilize.
When you select Rotation or Scale in the Tracker panel, you set two track points in the Layer panel. A line connects the attach points; an arrow points from the first attach point (the base) to the second. If possible, place the feature regions on opposite sides of the same object, or at least on objects that are the same distance from the camera. The farther apart the regions, the more accurate the calculations and the better the result.
After Effects calculates rotation by measuring the change of angle of the line between the attach points. When you apply the tracking data to the target, After Effects creates keyframes for the Rotation property.
After Effects calculates scale by comparing the distance between attach points on each frame with the distance between the attach points on the start frame. When you apply the tracking data to the target, After Effects creates keyframes for the Scale property.
When you track motion using either parallel or perspective corner-pinning, After Effects applies keyframes for the Corner Pin effect to the layer to scale and skew the target layer as necessary to fit the four-sided area defined by the feature regions. The feature regions should lie in a single plane in the real world—for example, on the side of a bus, on the same wall, or on the floor. The attach points should also all lie in a single plane, but not necessarily the same plane as the feature regions.