making simple shaded transitions

Hello,
I would like to make this type of transitions in Motion. Should be fairly straithforward?
www.motionvfx.com/mplugs-138.html

I have done transitions with different brushes using the Motion transition template.
Made a QT film from images I made and then applied it to the Motion transition.
Two layers and one clip transitions into another.

I'm wondering how to add the black shapes that move around.
Do I add them on another layer and have them fade with opacity?

I will be trying this out but if anyone has a tip it would be welcome.
Thanks.

Black shapes, very feathered edges, keyframe the movement across the screen. Keyframe the A (below the black shape layer) to wipe along with it. Keep the B layer at the bottom for the duration of the transition.