Multiple overlapping shapes can be combined into one shape by using MPSuperShape's Union operation. The Union operation works with shapes that have shared edges, as well as those that overlap. First, select the shapes that you wish to combine (red and cyan in this image):
Right click on the map to display the MPSuperShape popup menu. Select Union and MPSuperShape will combine the selected shapes where they overlap. For example, the above shapes will combine to create the following shape:
Note: In theory it is possible to create 'holes' using the Union operation, but MapPoint does not support complex shapes with holes. If you try to create a shape with a hole, then MPSuperShape will only create one simple shape. This will be either the perimeter or the 'hole' of the correct complex shape.