If you want to do a good job, just remove a few inches of soil (max 3") put down weed barrier cloth, put up your shelves (blocks directly on the weed cloth) and then shovel in your gravel when you are done. It doesn't have to be a lot of gravel - it is there just to look nice and prevent mud and weeds, as well as protect the weed cloth from you tearing it up when you walk on it. I have been to many nurseries who put down weed cloth, stack their shelves, and never do anything else. Do NOT dig a deep foundation so that the base of your shelves is below grade, because then you will be creating a mud hole. You will be watering your trees a lot, so you want your gravel to be at grade if not slightly above grade so that water will run off.