In my layout, I will use both... The stub yard is for making up trains and loading containers and trailers in the intermodal facility. A train can then go on a yard line which can access the main lines but is compleatly seperate, and compleatly connect the train there and set it out for mainline engines to get. An incoming train can also do the same, and the switchers can break that down, take the seperate peices to the stub, and then mix them around for unloading in the intermodal yard. To me atleast, it seems very prototypical and I really can't wait until I'm done to start railroading!!! A diagram of my layout is below and will show you what I'm talking about. The yards are on either side connected by a small track above the blue box. I know its not to scale, but it all works. I've drawn it to scale on my layout and everything i want fits.