Jacob, you have to do some playing around to get your settings where they need to be. It all depends on what type of setup you have. If you're using a rack, you can place the probe right next to where the heat cable is. Secure it with a couple pieces of electrical tape. Set the thermostat to higher than what you want your temp to be inside the boxes, because you have to make for the heat transfer through the plastic and whatever bedding you use. Do you have a temp gun? You basically need one to be able to keep checking your hot spot until it is where you want it to be. I (and the snakes) prefer 89 degrees. The cool end will then regulate itself. Mine is between 75-80.
As far as your basement, I had the same problem. Check Craigslist for a dehumidifier. Someone told me to do that on here, and it was very worth it. My basement is now 20 degrees warmer than it was before the dehumidifier. My temps stay perfect. And the air is much better down there. I dump like 3 gallons of water a day out that came from the air. I paid $75 for an almost brand new one that works perfectly. They're around $150 in stores. Hope that helps you out. Ryan.