Do you have 4 button, or 5 button Duo Therm thermostats?
The Furnace option on your thermostat is your Aqua Hot heat. Most Monaco coaches are set up with AC zone 1 up front, zone 2 in the rear, and zone 3 is the center.
This is programmable by removing the plastic shroud over the AC and then the small metal cover over the AC circuit board. The metal cover is on the right (passenger side) and held on by 2 small screws. The circuit board has dip switches that determine the zone number.
It may be possible someone replaced one of your AC Heat Pumps and not set the dip switches up properly (this is common).
Also, some coaches have only two furnace zones even though you have 3 AC zones, and most coaches also have a basement heat zone.
To reset the thermostat (required if you change dip switch settings):
1. Turn the ON/OFF switch (black switch on underside) to the "OFF" position.
2. Simultaneously depress and hold the MODE and
ZONE push-buttons while turning the ON/OFF switch
to "ON". FF should appear in LCD display until the
mode and zone push-buttons are released.
4-Button manual
http://bryantrv.com/docs2/docs/ccc.pdf
5-Button manual (Dip Switch setting Figure 8)
Duo Therm 5 Button 3109228.001 Troubleshooting
The electric Aqua Hot will use 12a and is not a good option on a 30 amp service. The Aqua Hot diesel burner smoking is no big deal. If you are cold, you can still use it as long as it doesn't upset your neighbors.
You can service the diesel burner yourself. It will need a new fuel filter and burner nozzle. You can purchase parts and get advice here:
RV Hydronic Heater Repair - Home
The heat switch in the toilet can be an extra Aqua Hot heat exchanger or an optional electric heater.
You can download legacy Monaco Owners Manuals here:
https://www.monacocoach.com/rv-owners-manuals
(They do not list the 2000, but the 2001 will be very close.)
Hope this helps.