MaYoKy:
First of all the Air Conditioning and the Furnace (heating) are 2 seperate systems, with only the thermostat being the major common component. There is some Furnace interface in the AC control circuit board.
The furnace runs on 12 volts DC, that is why you will find its wiring protection on the 12 volt DC fuse panel, instead of the 110 Volt AC circuit breaker panel. RV manufacturers want the furnace to be able to heat you up, even if you are not connected to AC power.
Now some questions. When you replace the fuse for the furnace, is the thermostat turned OFF? If this hasn't been the case try that first. If the fuse still blows without turning the thermostat to furnace, you have some sort of a wiring short in the power wiring to the furnace. If the fuse only blows when heating is called for from the thermostat, you might have a motor short in the furnace, which seems to be something I have heard of being common on these RV forums.
If the only thing that has changed since yesterday is the fact that the furnace ran some, I think your furnace needs troubleshooting. Is your rig new and under warranty??
Good luck!!!