That doesn't seem like a very good idea, considering you can buy an aqarium heater for $20-25 for a decent one. A waterbed heater isn't designed to be submersed, it's usually placed under the waterbed bladder, so I think it's a safety hazzard. I wouldn't do it.
I thought you could put down a piece of styrofoam or thin wood on top of the aquarium stand, then the waterbed heater, then the aquarium on top of that. The waterbed heater would be underneath the tank not in it. If you are familiar with a water bed heater you know it is flat and would fit nicely. I think it would evenly heat the whole tank.
Oh, I misunderstood what you were planning on doing. Actually, that might not be a bad idea. However, as I recently tore apart a waterbed, the heater's thermostat seems to have to be directly against the bladder. I'm not sure if it would get good readings under the tank. It would most likely have to be placed in the aquarium. That would be a good way to heat the substrate for circulation. You can always try it out and see how it works.
I believe people have tried the reptile heaters that stick underneath an aquarium and heat the glass. I also believe they were successul in using them, but I don't know if they come with temp. controllers. Another issue was that the reptile heater could have had a possibility of cracking the glass but I don't believe anyone had run into that issue. Anyway, the waterbed heater seems like the same idea. How large is the surface of the heater and does it come with a temp. controller or monitor?
You wouldn't want to use styrofoam, for sure. It's a thermal insulator. Glass is a descent thermal insulator as well, so it may take some time for the heater to effect a change in the aquarium. However, this may be a good thing as it will lead to a slow ramp up in temperature. If you need to support the aquarium above the heater somehow, use a sheet of aluminum from Home Depot. Wood is a bad idea because it could pose a fire hazard, and it will dry out severely and may crack. This might cause uneven support of your tank and damage it. Plus wood will absorb moisture from any incidental tank spills and going from very dry to sloppy wet will definitely warp your wood at the minimum.