Subbuffers! JCook was you able to get this working?
So yes I got it to work. Here is how I set it up.
1. In the layout setting I created two different face definitions because I have two characters, you can still do the left / right or top/bot with 1 definition.
2. in sequencer view, I added two layers below my main Matrix.
3. I added the face effect to each of these layers then selected my Face 1 for the top layer and face two for the bottom layer.
4. Once you have the effects on each layer select all of the effects on the top layer open the Layers settings, down in the window with the yellow box right click and choose halves - Right or Left,. In your case Top / bottom. Repeat for the second layer.