NOTE: the term programming in the following is used loosely. All you do is select conditions from a menu.
Yes, RR&co will handle it easily assuming all T.O.'s are with stationary decoders with detection blocks setup on the rungs, lead(s) track, etc., and have the signal light driver board (the sig driver board only drives the correct led from info received from the software). But why just control the yard? Why not the entire layout operation? You'll love it!
The key is the software must know where the trains are: thus the detection. The signal lights are programmed (software) to respond to the conditions you program for the block detection, turnout positions, and where a train is. If you have a route setup that runs through the crossovers, then the software will setup the turnouts in the correct position and give a signal light the color you want for that condition(s) (you have two, three, and four light capability, including flashing light). Note: It is usually advisable not to include turnouts/crossovers in the "physical" detection block, but they are still included by the software in all controls, routes, and schedules. The reason is this can become problematic in the computers control of routes and the reserving of blocks. You have to understand more about the software, but this doesn't present any problems.
You didn't say what Command system you are using. If it is Digitrax, then all communications are handled by the included LocoNet: from the detection board to the computer, to the light driver board, and to other ancillary devices. You will have to read about the Digitrax detection and sig board to see its compatibility with other manufacturers. Railroad&Company will work with most all USA companies and several European.
My layout is a large double car garage with ~1500 feet of track on three levels. All the mainlines are bi-directional. I have had as many as 10 individual trains manually running and three passengers on automatic at one time without a mishap. Each train and its route was being monitored by the software and the turnouts, crossovers, signals, and all traffic flow being controlled by the computer. Example: If someone failed to stop on a red, the computer would stop them and put them on hold until the red condition cleared. Blocks ahead are automatically reserved for a train when clear and the turnouts are set to the direction needed by the programmed route. Cool huh? It goes on and on. This software has been around a long time and was recently upgraded last year with more and easier features and now has even more capabilities to some very sophisticated operations. They even field tested it on the huge layout in Hamburg Germany
http://www.miniatur-wunderland.com/
As has been noted, signals and traffic control requires a lot of time for the installation, but you should always be patient and take your time to plan and understand the entire operation . Also, understand that this is a full hobby within model railroading. I have used most of this past year in getting mine setup to get a good operation going, but there are many things that I can do to make it even better. One thing for sure, be careful in your layout design and include many passing sidings and the use of blocks from the start. This is something I did not do as my layout wasn't going to have signals. I ended up having to install many more passing tracks and also reworking several areas of track. This wasn't a bad thing, as all the areas were weak spots in my operations to begin with.
Expense is high, but if you make your own signals, you can save bundles. Somewhere in this same category "wiring,electronics, DCC", you will find my thread on making your own signals. There are many options available other than what I have chosen, but if you are committed to have a fully functional and automatic signal/traffic control system, this is what I have found to be the best with the most.
EDIT: The manual for Railroad&Company is about 300 pages. You can download this and study parts of it or just read it on your screen. This may answer some of your questions.
