The thermosensor/thermostat for our basement is in the waste tank bay in front of the passenger side rear wheels, along with several Aladdin modules, solar panel circuitry, water pump enclosure, etc. The bay sector is not adjustable like the other zones, so no thermostat as in the living areas. I believe it kicks on the bay heat (you can see the exchanger in the bay) when ambient temps get into the 40's F; the exact number I don't recall offhand, but I read it in one of my manuals a few years back. As long as the hydronics is on, and doesn't fault somewhere along the line, the bays are protected from freezing. The temp. in the bay with the AquaHot unit itself will obviously get warm just because of the burner there.
If it seems the waste tank bay isn't heated, it's just because it's set in the 40's and not the 70's like you set the living area at; whether the bay exchanger is on or not shouldn't be tied to your living area thermostat.
Joel