The red light will still give off heat. But supposedly the red light doesn't disturb them at night like a white light will. Another option would be using a Ceramic Heat Emitter, if it is needed.

The only thermostat that I know of that will control 2 heat pads independently is the Herpstat II by Spyder Robotics. Another cheaper option would be to get something like a Johnson or Ranco and use it to set and control the warm side UTH. Then plug a rheostat into the thermostat power strip and use it to control the cool side UTH. Or you could just get 2 thermostats. There are a few ways you can do it depending on how much you want to invest in your set-up...