I had two 500watt glass fish tank heater that I put on the bottom to keep it from freezing over. During the winter it got below 0 a lot of times and parts of the pond would freeze but the heater kept a nice large open circle in the pond, which i thought was ideal.
I asked the question because I wondered if it was possible that an aquarium heater on the bottom of the pond would get hot enough to melt a hole in the liner if it was in contact for an extended period of time. I don't know if by "at the bottom" you meant near the bottom, or literally on the bottom. Your fish dying and your water disappearing may have two separate causes.
Also, I am near Chicago also so I know the kind of winter you've experienced! I am sorry about your pond and fish - you've already gotten some good suggestions. Hopefully the answer is an easy one!