The loading dock should be level with the floor of the boxcar, at least within a few scale inches. A moveable plate bridge would be used to allow a fork lift to go back and forth. Obviously, in our little model world, that's not a real problem, but visually it will make more sense to show that relationship.
Also, just to make the problem worse, the siding should sit at a lower level than the main line, so to really make it look right, you'll have to whittle another 1/8 to 1/4" from the bottom of the building.
Lee