Try some of the tips Mykee stated, but also try placing your fans at opposite ends of the incubator blowing in opposite directions.
If you have one at the top right blowing down you will want the other one positioned on the bottom left blowing up. This will create a better current for the air to follow. If you place the fans along the edge of your incubator and your tubs are positioned in the middle of the incubator you should have enough room for air to circulate around the tubs.
Also, try Mykee's tip about using smaller egg boxes. Usually people tend to use larger boxes than is necessary because they are planning for bigger clutches. Try to keep more than one size of tub on hand. At least one size for smaller clutches (~1-6 eggs) and another size to handle the medium to large clutches (~7-12 eggs).
As long as you are filling the "empty" spaces in the incubator with some sort of extra thermal mass you should be fine using a combination of tub sizes. Generally, the easiest way to go about this is to fill used (and washed) water or soda bottles with water and place the bottle(s) in the empty spaces in the incubator.
Every incubator will take tweaking before you can iron out all of the kinks and the great part is, if you have a homemade incubator you will get a chance to tweak it a little more next year (always happens to me). I prefer my homemade incubators to those I've purchased simply because I can disassemble and monkey around with the parts without feeling like I have the potential to break a $300-$1000 piece of equipment.