One option would be to create the matte in Photoshop.
Create a document the same size as your sequence.
Cut or remove sections to create matte.
Save for web and devices/png-24 /transparency/ interlaced if applicable
Depending on the transition and how many elements will show in the matte you make want to make a nest
with a matte on the top layer and video/stills scaled to fill the holes. The motion tab for the nest will allow you to move it on and off with key frames.