I have a three burner Mankel forge with a blower.  It uses a lot of fuel and I don't need all three burners all the time.  If I want to use just two burners, which ones should I use and which one should I turn off?  Is there a problem with the heat going up the turned off burner? I have the openings blocked off so the fire comes out of one end like a tube.  Do I turn off the one burner nearest the opening or the one farthest back  in the tube?    

Put a temporary wall in blocking the unused 3rd burner. You do not want exhaust gases going up the unused burner. You could also block it off shoving some kaowool up the inside of the burner.