I left the tray out of the front cube, so all their droppings fall straight to the ground. The rear cube still has the catch tray, which I felt was necessary for security because the roosting area of the rear cube is not protected by the run fencing (see photo).
As for cleaning the front...
There's plenty of ventilation designed into the cube already. 4 vents on each roof panel, 2 vents on each end panel, and the roosting area is completely open underneath (I have the tray removed on the front cube. I'm not concerned at all, it's very comfortable in there.
I wanted to share some modifications I made to expand my Eglu cube. I'm entirely new to chickens, and I bought an eglu cube, 10 chicks, 1 guard goose. I swear, before I ordered the cube, I thought I'd read that it would hold 10 chickens, but after building it I realized I wouldn't be comfortable...