Yes. Like Elaine said above, the rocks can and should be left in place if all you have in that spot is loose, friable or "good" soil. If the planting area hadn't been disturbed and then fixed with loose fill your crowns most likely would have stayed above the soil line. Here, we've learned (the hard way
) to plant the root ball in and on top of a mound of native soil (preferably soil that hasn't been disturbed) , return chunks of native soil to the hole, up against the root ball, and then add a mix of native soil and compost to fill the outer edges of the hole. You want those roots to travel out toward the goodies, not just sit where they are.
What happens, and you see this all the time in subdivisions around here, is that once the planting hole is filled with "goodies" the tree/shrub won't be as tempted to send out those long and lovely structural tap roots to hold it up. First storm that comes along after any cables are removed, and that tree is down and done.
In my opinion, additional compost/goodies really shouldn't be added to the base of trees for a year or two, or at least not much if any nitrogen, and don't water when it doesn't need it. A regular watering routine will cause short-rooted plants as well. You want the roots of these very large and potentially dangerous plants to root well, and they do that best by having to hunt a bit for what they want.
Shrubs are easier...just keep those crowns a bit on the high side and mulch/compost around them from about 6" or so from the stem outward in a circle the size of the plant's circumference or just a bit more.
