Let's go back to the real question, before we add more answers than were asked.
It makes no difference whether you put the ammeter in series with the middle rail or the traction rail. You are using alternating current, and the meter doesn't care which rail you use, or what color the leads are.
To find the current in any circuit, you need to isolate the exact component or circuit that needs to be measured. In your case, insert the meter as close to the track as possible. That eliminates any readings from other parallel circuit return wires.
RR Fan Ron is also correct in his advice. It is true that if you put the meter in series with a major wire that supplies all the "return" current from several different "hot" sources, you will read the total current being drawn from all those hot sides. But that's not what you asked, and it appears that you have a good understanding of how the meter should be used. Always remember to isolate the circuit.
Gun Runner also has a good idea: if you want to have a nice-looking control panel, use a separate analog meter in each track supply. If you are just experimenting to see whazzup with current draw from various locos and passenger cars, then the digital test meter is the way to go.
Many digital meters have an internal fuse in the high current circuit. Are you using a digital or an analog meter?