Lets try to think it threw.
One res and one pump:
we have the pump in the res going to the top tray. The drain on the top tray going to the bottom tray. The drain on the bottom tray going to the res. Now when the pump turns off the top res drains back threw the pump to the res. So the top tray is not a problem. The bottom tray will now stay full since it does not have the pump to drain threw. It will stay flooded up to the drain. This is a problem. Unless we can figure a way around this you will need two pumps. You are right. Working around the light is easy though.
To fix the problem you could have a second drain in the bottom tray that is just a smaller hole. With no rise on it. The tray will still fill up as long as the drain from the top is larger than this small hole. Still have a second drain on the bottom tray with rise.
Here is just an idea.