A look at using the standard MochaAE offering in After Effects, for a fairly straight forward method for removing items from a shot in After Effects from reTooled.net showing some basic tracking in MochaAE. Check out the tutorial for adding logo or type to a moving shot using mochaAE and After Effects here.

…Using After Effects, Photoshop, and Mocha to do incorporate and track a title or logo into your footage…

In order to add elements to a shot, you need to remove what was previously there, and here Josh shows how to use Photoshop to paint out the area where the new elements will ultimately reside. Although MochaAE comes with a purchased copy of After Effects, Imagineer also provides Mocha Pro, which has a handy remove module just for these types of tasks, and it is a HUGE time saver in the long run.