Shadows are always a pain. They all have to be on one layer so as to not cause the overlapping darker shades. Then you need another layer for where they interact with different levels of the city (a layer for ground shadows, a layer for shadows that fall on flat planed roofs/walls - because they will not go as far out as those on land and since they are higher they are closer to the object thus they are a tad smaller, and a layer for angled planes, like slanted roofs, which will cause distorted shadows). Blah, way too much to think about so shadows are always a pain. Two suggestions: 1) put a copy of all of your shadow-casting objects on one layer, at the bottom of the layer stack, and use that to make the shadows - and 2) make all your shadows solid black, merge those layers together, move to the bottom of the layer stack, then reduce opacity to suit. Maybe I should do a tut on shadows.