IN my expirience so far, the manometer is used to check the pressure in the firebox.
There are at least a couple good reasons for this.
1. We ALWAYS want a negative pressure in the stove/furnace so Carbon Monoxide doesn't escape into the living environment.
2. Based on the pressure in the firebox we can better adjust our draft thats feeding the fire. For example a .06 pressure will pull MORE air thru the SAME size hole (draft opening feeding the fire) than a .03 would. Keep in mind these are negative pressures. A barometric damper helps keep a more consistant draft pressure in the firebox.
So given the above conditions that we want to monitor the most, the best place to take the reading for the manometer is IN or just SHORTLY after the firebox but BEFORE the manual damper and/or barometric.. So proper sequence is Stove/Furncace - Manometer - MPD - Baro - Chimney.
Putting the manometer after the MPD will give you a false reading about the condions in the firebox. As a matter of fact, I would say this could be dangerous since you could be showing a neg pressure after the MPD, but if its closed too tightly, pressure in the firebox could go positve. Then you have CO leaking into your house. It most definately DOES matter where you take the reading from
If you can't get a negative pressure reading at all or its not like it used to be there are many factors. There could be a blockage in the chimney OR the chimney has developed a gaping hole (rotton metal) OR atmospheric conditions outside have changed like wind speed/direction or temperature.