First, I have no idea what program you're using. I'm using Photoshop.
Second, I read your post and thought it would be fun to try. I used three different methods to try to get a look that I thought you were looking for. I really like the colors that came out of the Red>Blue bridge. The Colors on the Green>Red are more pronounced. My favorite (and my wife's favorite) is the Blue>Yellow Bridge, though that might just be do to the delicacy of that particular bridge.
I think that it's pretty obvious which bridge is above the other. That's partly to the stroke on the outside edges and partly to the outer glow and shadow on the highest bridge. With my particular type of mapping style (Cartoonish Realism) it's not hard to see what's above an other, but a more realistic drawing would create more problems.
Anyway, it took me about 45 minutes, and is easily replicated. Let me know if you want a tut on any of the different types of bridges.