Dear Catarina,
I suggest that you try to understand better your concept, you need to be clear with hydrological relationship between all your geological layers. If I understand correctly : your layer 2 and perhaps layer 3 could be unconfined and confined depending hydrogeological circumstancies, and your layer 1 and layer 2 are not present on all you surface?
Without drawings or scheme it is sometime difficult to be sure... :-\
Your layer 1 covers all your surface, but where it desappears, I suppose that the tickness of this layer is very small (10-15cm) (you could check it, it depends of your model design), then there you but the caracteristics of underlaying geological layer. It is the same with layer 2.
I suggest that you put free&movable for slice at the top, fixed for the bottom slice and unspecified for the rest. In the problem definition menu, check the help and I think you could understand and solve your last question. It depends if your cells in the layer 1 could be dry and this depend of the geometry of model etc...
I hope this help you, feel free to ask more details :)
Best regards