* place both materials on object;
* activate alpha channel in second material;
* add the color shader to the alpha channel;
* animate color in alpha from black to white to reveal the underlying material.
Basically do the same thing but using the layer shader in each channel you want to change, i.e., by animating layer visibility.
In order to do that you have to right-click on the word Layers and choose "show sub-channels" from the context menu. That gives you access to sliders that can be animated.