The boxes you see, actually, I put holes into them shortly after setting up. I was noticing too much condensation in the boxes. And I was reluctant to place an open dish of water directly into the incubator, because I do not like the idea of mixing high humidity/water droplets, with flexwatt and electricity. So on a whim, I melted the holes into the boxes, and it helped to get rid of the condensation and even things out in that department. I am nto sure that holes in the boxes would work for everyone, but it worked for me.
I should add; my substrate was a mixture of larger-particle vermiculite and perlite.