Applying different color keys to one layer in AE
You'll have to make as many duplicates of the layer as there are colours. Apply the appropriate key to each copy, and place the layer you want it to reveal beneath it. On the revealed layer use a track matte, and set it to &quot;Alpha Inverted…&quot;. This will hide the keyed layer and use its alpha channel (transparency) to reveal the layer underneath it, but only in the transparent areas.
Your layer stack will look like this, but for any areas not in any of the keys you'll also need a copy of the original layer at the bottom of the stack: