Here are some things I keep in mind when designing a yard:
First, the main purpose of a yard is not a to have a place where cars are stored, it is a to have a placewhere cars are sorted, and consists are made up. If you're planning on using a yard as a place to store cars, then you need to build it bigger.
A second thing to watch for is placing yard tracks too close together. In a real yard, the tracks are usually on 20 foot centers, that is, having enough separation that one can drive a motor vehicle between them.
A third thing to watch for is having your yard too short, particularly the junctions / switches at either end. Most model yards have ladders which are at a much steeper angle than yards of the same size in the real world. A modern yard, when the shortest cars are about half again as long as they used to be, has a ladder which is at a narrower angle than in years past, when the typical car was generally shorter.
Use your favorite mapping program, such as google maps, and study the layout of real rail yards of about the size you intend.
ns.