Both the stack draft and the burner air quantity affect the combustion efficiency by working on the same variable - the combustion air and also affect each other. So you have to adjust both simultaneously to get the right draft with the optimum CO in the flue gas. There is an article in Hydrocarbon Processing May 2006. Vol.85 No.5 page91 titled Optimizing O2 levels in fired heaters - by S. Patel which gives a simple method to do this.
Best wishes