Chuck,

I generally use 12 qt. or 6 qt. boxes depending on the size of the egg clutch. Since my incubator is a former refrigerator, I use a tub of water in the bottom to help keep the humidity I need inside the incubator. The fan blows across the top of the water tub so that as the water evaporates, it is blown around the inside. The egg tubs have no air holes in them. I use a really wet perilite on the bottom and put egg crate on top of that. The eggs go on top of the egg crate.
As far as gas exchange, you will get that about every other week or so when you open the tub to check in on the eggs.
Using the set-up that you have, I do not think you will need a tub of water. You should have enough in the egg chambers.