Don't know how you are progressing - but I found I only had trouble with lighting when placing something like a map entity down on floor tiles which where fully lit. If I did then definately a material definitions was required to correct the lighting (with the ambient settings way down).
Here is a shot of some map entities that are correctly lit without setting the unlit flag or defining a material. There are no blocks beneath these entities so no adjustments to the map entities were required. (The red indicates some missing floor shadows I now have to fix). The ambient values have been decreased for the sprites and models. They also are not using any material defs.