I mostly have the fine sponge and wool in the top tray as then I don't have to pull the whole thing apart just to clean the fine mechanical filtration.
I'd love to know how much free O2 is left in the water as it exits the filter? I suspect that it is getting very low, another reason I like the bio media near the beginning of the filtration system to maximise the O2 to break down ammonia, nitrite and nitrates