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The heaters are hooked up to your engine's cooling system (the hoses carry the hot coolant out to the heaters and back), so normally they only function when the bus is running; when parked, they'll just be taking up space and you'll still need an alternative source of heat.
It is possible to hook up a separate diesel heater for the coolant, which would allow you to also use these heaters while parked. Pretty expensive, though, and the plumbing is not that simple. They do have a side benefit, though, in that they can be used to pre-warm the engine before startup on cold days.
Removing the heater would theoretically make the back of the bus colder, but with a shorter bus the front heaters will probably be more than sufficient. I drove my 11-window bus in below-freezing temperatures last winter and the front heaters kept me nice and toasty while driving - despite having a wide open 8'x8' hole in the floor in back.