Djekspek - Thanks a bunch, my man! Your ISO dungeon was a huge inspiration and made me think this was worth trying! I agree that multiple levels can be tricky, but they are also part of the beauty of isometric maps, I think. I considered using slightly transparent materials, but I think when all is said and done, it looks cleaner to have 'cut out' bits, like in your dungeon. I think I might have figured out some tricks for doing post-render shades in PS, too: you can output a separate image with the shadows alone on it, and then apply things like gaussian blur and fill in other areas, set it as a 'multiply' layer. I also just discovered that you can 'paint' an object with a simple transparent .png image as the material and it will be transparent but still cast shadows--A near 'glitch' that will allow for more consistent lighting with roofs that are 'there' but not there. I am still looking into other plugins for adding multiple light sources (and hopefully soft lights): I'll post if I can find a free one.
All in all, I am loving Sketchup. Definitely preferable to graph paper.