Before baking from a high poly to a low poly, if you would like an ID map (see Texture Types), first apply your different materials to your high poly model. Then, when baking, underneath the ID settings select “Materials”, and it will bake an ID mask based on the material assignments of the high poly.
For baking, it is easiest to set “Match” in all applicable areas to “By Mesh Name.” Doing so will set-up a pseudo cage for each mesh element that may be controlled by the max and min frontal/rear distances (or occluder distance in the case of ambient occlusion) and reduces the chances of error.
