Loading at the tipple does still take place. It was more prevalent in years gone by than today, however. Flood loaders will generally be used more often for unit trains (all coal cars) that pretty much go from Point A to Point B, or where terrain prohibits loading at the tipple.
Tony Koester wrote an awesome book on coal operations. As I plan to feature coal on my layout as well, it was one of the best purchases I made. It really lets you get a feel for how things operate.