sstlaure and T-Man have basically said it all. But Tkruger, let me try to zero it in a little bit further. I'll try to explain in a simple format of how this is used. This panel and what goes with it were designed basically for what is called the COMMON RAIL method.
Okay, look at the front of the controller. At the top you will see three little silver panels side by side with screw holes in them. The one on the far left has the letter "C" under it. This is where one end of the COMMON wire attaches. Under this method, the opposite end of the common wire is attached to the inside rail, your choice of where. This rail then becomes the COMMON RAIL ( the hot wire) for the entire layout, with no breaks or insulated joiners anywhere on it throughout the entire layout. In other words the rail itself acts as a contiuous power source, via the "common wire."
Now look at the panel once again. On the edge of the left side of it there are two little silver panels (one above the other) near the top and two near the bottom. The variable DC wires of each transformer are connected to these with screws. One transformer is connected to the top two and the other transformer is connected to the bottom two. Make sure that the wires connected to each transformer are in the same order on the transformer and also on the controller for each. In between these little silver panels of both the top and the bottom, you will see little holes. This is where you conect this controller to your control panel. The right side of the panel is a mirror image of the left and connect your screws to the control panel in the same way as the left.
From here you're going to need what is called a SELECTOR. This is what it looks like. http://a248.e.akamai.net/origin-cdn...5b/v/vspfiles/photos/ATL-215-2.gif?1313757924
This panel is where the other wires governing each insulated block connects to. Place this selector panel up against the right side of the controller panel exactly the way that sstlaure has shown in his top photo. You will notice when this panel is alligned with the right side of the controller that the little silver panels of the selector (one near the top and one near the bottom) are in perfect line with the little silver panels on the right side of the controller. Atlas makes what they call a double spade connector. This lays perfectly in the spaces where both the selector and the controller allign together fastened with screws. Look again at the photos provided by sstlaure. At this time don't pay any mind to the second controller in his photo because it is not needed for just a simple hook up. Your controller and selectors panels should look exactly like his, minus his second controller.
Now connect a wire to each of the circuit breakers at the top of the selector. Each of these will control an individual block and the other end of each wire coming is connected to the outside rail of each corrosponding block. Insulated joiners will need to be used on this rail thus insulating each electrical block from the other.
On the left side of the face of the controller the are two sliding red switches. The top one says CAB A and the bottom one says CAB B. These both control the direction of the train by each transformer. To test, set the train on the block that is wired to the first breaker on the selector. Push the first breaker sliding green button on the selector panel all the way up. This allows the train to be run by the transformer that's wired to CAB A. If the breaker on the selector is pushed all the way down, the train will be operated by the transformer that is wired to CAB B. This same rule applies to all of the breakers. If any of these green sliding switches on the selector panel are set in the middle of the panel, rather than in an up or down position, The power will be cut to that particular block.
If when testing, the train runs in an opposite direction with one cab from the other, then set the direction button on one of the transformers to the opposite direction. This will ensure that the trains will run the same way when both buttons are set to the same direction on the controller without having to rewire anything.
After this, whenever a different direction is desired, set the direction using one of these red sliding switches and not the directional switches on the transformers. This is only a very basic method. Atlas makes a very good tutorial on how to wire reverse loops, turntables, tunouts and much more. It may sound very complicated now, but it's really not. Here's a picture of their book and the linc to where you can get it. http://a248.e.akamai.net/origin-cdn...b/v/vspfiles/photos/ATL-BK12-2.jpg?1313757924
Where to get it. http://www.modeltrainstuff.com/Atlas-12-The-Complete-Atlas-Wiring-Book-p/atl-bk12.htm
I hope that I haven't made any of this sound too confusing to understand, as I tried to simplify it in my explaination. The book is extremely easy to understand and it also shows very easy to understand diagrams as well. I refer back to it from time to time when doing different wiring proceedures. It has really served me well, as I have used the Atlas common rail system ever since I began model railroading. I Hope that at least some of this has helped.