When you say grill grates, are you talking about the grates /racks that come with the grill or the GrillGrates customer made for specific grill that are used for searing.
They way you cook various dishes depends upon what you are cooking. If you want maximum smoke flavor, you want to place the protein directly on the grill rack.
Sometimes you do not want maximum smoke flavor. For example, when cooking salmon, I use a cedar plank underneath the fish. Smoke only penetrates from the top.
I plan to cook my Thanksgiving turkey on the Trager placing the turkey in a large pan to catch the drippings, but using a rack inside the pan to raise the bird off the bottom of the pan so everything gets smoked.
There is no right way or wrong way to cook. Do whatever works best for you.