You need to decide what you will use to obscure the logo. The simplest way is to place something else over the top, another more complex method is to blur just the area of the logo.
In either method, the basic principle is to position the overlay using motion, and then use keyframes in Motion to track the movement of the logo - if necessary frame by frame.
In the second method, the blur is applied to a second copy of the logo and a track matte used to track and expose only the logo area of that blurred clip.