The worst thing you can do is cover a tree's roots with ANYTHING! Soil, rocks, stones, more than 1 inch of mulch... yeah... anything. It would be like putting a pillow over your face. You would suffocate. So do they. Tree roots NEED AIR!
Take the Healing Path Step 5: Always practical, when you do your needed garden or tree care chores, having this holistic approach will be both respectful and successful. You will be working in partnership with Nature.