There are many others here more qualified and able to describe this much better, but I'll give it a try. For measuring voltage I think it's good practice to use red for the positive (center rail) and black for common (outer rail). Our O gauge three rail trains are almost always AC so it will read the same either way. This is called polarity and it does matter with DC voltage. Red is positive and black is negative or common. Of course the meter inputs are marked and the leads need to be connected to the meter accordingly.
Probably the most important thing to remember when using a meter is to select the proper meter dial setting and range for the voltage, AC, DC, resistance or continuity, current, etc. that you are trying to measure. Measuring voltage with the meter set to resistance (continuity) will either blow the meter's internal fuse or ruin the meter if it isn't fused. Don't ask me how I know this...(but mine was fused). 
