I worked with a similar setup this weekend. I have some solutions to what you decribe, but I am pretty sure that Joris will say that we are complicating it too much ; )
This setup has only one single slice. I din´t even needed one. I did it to better fit images on panels.
Course, in that case, all client´s custom content was ready edited/produced divided as panels.
Consider the compostion and your frame size as the total area of all panels.
So, the lower 3 LCD panels content clip was produced leaving the rest of the frame with no information, but the Alpha Channel applied. Just put that in the top layer. Presto!
You can also do that with 2 slices. You can setup a bigger composition and place your logo content in a clear area. Setup a slice to that area (logo area) and then transform it, move it to the desired location/screen.
But my guess is that Joris would just load the logo content in a layer and adjust that layer settings to move it to the proper size and position. And put it on top of everything. ; )