Scale City Designs (http://www.scalecitydesigns.com/) makes and sells shims that are exactly the same size as the Kadee box in 4-5 different thicknesses, thickest being 1/16 inch.
You should settle on a coupler heigtht, and then insure that all cars couplers on both ends are that height. The simplest thing to do is buy a Kadee coupler gauge and use it to set all cars at that height. If you choose some other height, you should make your own gauge to be able to consistently check and measure if couplers are mounted at a correct height.
I think you have been advised to check for dips and bumps and too quick transition from level to grade or grade to level.
With Kadees, I am going to guess the coupler head is about 3/16 inch high. I think 3 rail couplers are 1/2 inch in height. So with a kadee if there is a track condition that causes one car to rise or drop 3/16 inch vs another, they will uncouple.
You can get away with some differences in mounting height, but not nearly as much as with 3 rail couplers.
