Assuming you have two separate holding tanks of equal volume, the first being polluted water with food poisoning from your lavatories, the second being filtered water, it's quite simple to maintain temperature.
If they're the same volume, your first tank will be the sum of the heat deleted from the second tank using a thermo aquatuner. The device is a zero-sum heat transfer, so equal volume means equal heat transfer.
Thus, if you're inputting clean water from your water sieves at 40°C, you can raise the temperature of the polluted water by up to 40°C through circling the clean water. Personally, I prefer to limit my aquatuner's output to 5°C water to avoid accidental freezing, as I've found variance of up to +/- 3°C can occur with stopping and starting the input, depending on the volume in the pipe.
Thus your polluted water can easily gain +35°C, and assuming your polluted water input is above 30°C polluted water (pretty easy when you use water as heat sinks for high temperature areas), you've got a perfect germ killing tank that doubles as a heat deletion tool for your base (since any heat in the polluted water above 40°C is deleted when it's sieved).
If your polluted water tank runs too hot, the best option I've found is to destroy the heat gained by sinking it into your electrolyzer input reservoir. It's a good idea to dump heat from your electrolyzer output back into your water input anyway, especially if you're using pre-cooled purified water from the system above, as the electrolyzer can also delete heat if you're clever with the output piping.
Out of curiosity, what design do other people use for their bases?
Personally, I like 16 tile wide rooms, with 4 tile high ceilings, and 2 tile wide shafts between them to allow a ladder and a pole for transport. Does anyone else use something different?