This site here has helped me a lot.
http://www.vetmed.auburn.edu/%7Esmithbf/BFSpages/LDSIGprimer/TOC.html
You'll find a lot of answers on there.
As to the size your yard should be, your trains will dictate that. Unit trains tend to be longer, therefore they need bigger yards. Old time and shortline roads run shorter trains mostly, so the yards can be smaller. Another factor to figure in is the volume of traffic the yard will see. More volume = Bigger yard.
I had this same kind of question a while ago until I found the August 2006 MR issue. On page 24 there is a nice explanation of how yards work and what key parts are needed. There are also a couple of track diagrams that I used to design my small yard and I've been very happy with the results. If you can't find this article check out "Track Planning for Realistic Operation", second edition. There is even more info there. I hope this helps!
I also should have told you that
One will be used for loading and unloading container carsTwo will be for storage.