Advice For Heating Home With Multiple Heating Zones?

You didn't mention what kind of furnaces you are dealing with. We have a two story house with a gas furnace on each level. If we open our upstairs hall door, the heat will rise to our upstairs too and that thermostat will not kick the upstairs furnace on. But it will make our downstairs furnace run constantly--it isn't the proper size to heat that many square feet efficiently. Doing so continually will cause problems with that furnace making it wear out quicker, so in our case it would be a very bad idea.

The upstairs pipes probably wouldn't freeze. However, during really bad ice storms, we've had some pipes freeze in our upstairs bathroom with the upstairs furnace on. A lot would depend on your weather conditions, the layout of your home, whether you have a basement or crawl space, and how insulated your home is.