I hate to dig up an old post but I can provide you with a lot of information concering real-world operations. Depending on the type of train you have, you've got a few options to stop it. Most engineers I've ridden with will use the "stretch braking" method. This is when you use the automatic and throttle to stop the train. Typically, when you need to start braking, you'll make a minimum reduction followed by bailing off your independant (releasing the brakes on the locomotive consist only). After the minimum set is finished exhausting, you make another reduction, this time a 10 pound set, and bail off again. (Usually set at least 10 pounds on the automatic before releasing to avoid sticking brakes)
By this time, the brakes should be setting up and you should be slowing down. When you make the first reduction, it's a good idea to be in throttle power as this will keep the train stretched out and prevent the slack from running in when the brakes set up. You can use variations of this method depending on your train. A good trick that works for slowing short trains (only short trains) is to go straight to a Full Service, wait until the brakes start applying, and then kick it off. This will slow you down, and because the train is short, the brakes will release before long. Just remember that the brakes take time to set up, and Trainz does an excellent job of modeling air brake physics. Much more so than MSTS, and I use both sims.
The automatic brake typically has six positions besides the release position: 'Minimum', '10 Pound', 'Full Service', 'Supression', 'Handle Off', and 'Emergency'.
Also, the independant brake is very useful for stopping a train. Just remember to make slight applications to allow for slack adjustments and to avoid skating.