Allison, your garden sounds lovely.* I'd love to see pics.* Just be sure that you haven't added more then 2" of soil over the roots each year so the tree roots have time to rise.* Most tree roots are in the upper 12" to 18" of soil.* The rootflare of your tree should be visible and no soil or mulch should be placed against the trunk.* If your tree looks like a telephone where it meets the soil line instead of flaring out, it's buried too deep.
When weeding, the best way to make sure you are removing a weed and not a valuable plant is to pull on it. If it comes out of the ground easily, it is a valuable plant.