Here is a PDF for heater.
The 12V fan cycles with the furnace when its on and shuts off with furnace when heat level is reached.
The 12V for fan comes from control board of furnace is there a board on the old fan that you may need to place on your new fan and when furnace is on do you feel warm air coming from the heat hose?
The fan is only an aid to push more warm air into your lower compartments.
The new fan needs to be same current draw as the old one.
What is wrong with old fan?
I see nothing in PDF that mentions a 12V fan in duct tube may have been added by MFG.
Did you try reversing the wire leads to fan?
Welcome to irv2 by the way.