Have a look on this website for lots of info on how it is done for real:
http://www.railway-technical.com/index.shtml
What you could also look into, is books on railroad operations that are aimed at HO scale modelers, there are many such books which detail exactly how things are done, and much of this relates to the kind of thing you'd do in a train sim too, for example this one:
http://books.google.co.uk/books/abo...ad_Operation.html?id=orbWT5ZnLOcC&redir_esc=y
That's a pretty good book if you know very little about the day to day stuff, I in fact used that to plan out some of my own HO scale East coast model railroad, and it was a big help in clarifying what happens with boxcars and such and how they get moved around.
Worth a look too of course if you are into protypical US stuff, is Trains magazine, which is a mine of useful info on how the real things operate:
http://trn.trains.com/
As far as slightly more dramatic, but still day-to-day stuff occurrences are concerned, things such as broken couplers, hot boxes would be more typical little dramas than the kind of things which make TV programmes and movies. Taking cars out of a consist and leaving them on a RIP track so that welding repairs or some such can be done on them would be the kind of thing you might see. The advent of trackside hotbox detectors and stuff such as General Electric's Locotrol MU system means that screw ups such as stringline derailments and broken couplers are now much rarer occurrences than they used to be when primitive means of power application from helper locomotives used to be conveyed over radios or even signals on the train's horn, but they do still occur of course.
Whether one can simulate all that kind of complexity in Trainz is another matter, although certainly Trainz does handle broken coupler simulation to some degree, but you can definitely simulate prototypic movement of rolling stock with the info in those links I pointed to.
Al