When planting shrubs or trees you always need to be aware of the crown of the plant. Whether your plant is coming out of a container or is Ball and Burlap, you should not assume that it has been planted at the right level thus far. The crown of the plant is where the trunk turns into roots or where the trunk expands (then seperating and turning into roots.) If you have roots coming up in the soil then most likely you will need to do some excavating to find the real crown. I will generally do this only with larger plants so that I do not risk disturbing too large a percentage of the root ball.
In this photo I am planting a Cornus mas (Cornellion Cherry) and I needed to excavate about six inches into the top of the root ball. The little roots that have started on the trunk will never be substantial so I went down until the trunk began to expand.
The concern with planting trees and/or large shrubs with the crown too deep are many. The biggest is the likelihood of rotting out the trunks. Moisture builds up with no air circulation and microbes go to town on the living tissue of the trunk. Another problem that you are setting yourself up for is girdling the trunk with roots. Just like in Evil Dead when his own hand gets possessed and tries to kill him; the roots of the plant will go wherever there is soil. They will sooner or later go throughout the surface of the soil and expand as they age. This will interfere with the vascular system of the plants trunk and prevent it from being able to transfer nutrients and water to and from it's canopy. This can take anywhere from a few years to many years to seriously affect the plant. For trees this is a big issue because you wait so patiently for them to grow to a certain scale and stature. Often when they die no one knows why, but much of the time this simple observation could save have saved it from dying prematurely.
