You don't want ANY standing water. Tilt your entire tray by sliding a piece of heavy plywood and a couple 2x4s under there so that it drops an inch or two from back to drain. Puddles lead to slime, rot, and yes oh yes the disgusting fungus gnats. Blech.
If you can, swap out the black plastic with a sheet of panda film white side up to both reflect mroe light and keep the inside from heating up. Heat + standing water= slime and gnats much faster than without the added heat! Just like an oven, baking up yoru next batch of disgustingness.