I had similar questions myself about the temps and setup as ours was very similar. I ran into someone from this forum at Repticon Atlanta today, MasonC2K. He took about 10 minutes out to talk to me even though he was really on a tight schedule, but those 10 minutes were invaluable. Thanks Chris, it was really helpful.
As he described it, have the thermostat probe about the center of the incubator but not in a tub. Either hang it or place it directly on top the tub if you just have the one clutch as I do. If you have more then go back to centering it among them as best possible. With regard to thermometer probe placement, he also said that recently he found some variances in the thermometers as he tested 4 of the same kind and had 4 different results. So he recommended using an infarred temp gun to check the tub temps when you open it for air exchange. I went and picked one up from HD for about $40 and after shooting temps inside the tub and incubator, I found that I needed to make some small adjustments. If you compare the temp shown on the thermometer to what the temp gun is showing, then you will know to what degree it is accurate or how much it differs. You can keep the thermometer probe in the tub. As long as the variation, if any, stays consistent when you check temps with the gun, then you can guage/monitor it with the thermometer in the interim of opening the tub for air exchange.
I believe I am on the right track now and I hope this helps answer your questions a little more thoroughly.
This is all sounds good. But I wonder if placing the thermostat probe on the inside will also work. I mean by placing the probe in the tub, you are heating it to the exact degree that it needs to be.