There is one fan motor in your furnace, but two squirrel cage fans on either end of the motor shaft. The large fan circulates the return air through the heat exchanger and back into the heat ducts. The small fan take outside air and blows it through the combustion chamber and blows out the exhaust pipe. Either your exhaust pipe isn't hooked up properly, the heat exchanger has a hole in it, or some of the return/heater ducts aren't connected properly. Since you've had the unit out of the RV, hopefully all the ducts are properly connected. If the flame is properly adjusted, there shouldn't be a lot of soot in the combustion tubes and exhaust. Spider webs and muddabber nests can be an issue, but you've blown out the tubes.
Next, go through the linked manual and Service manual:
http://www.atwoodmobile.com/manuals/...0SP%201.08.pdf
http://bryantrv.com/docs2/docs/hflamefurn04.pdf