Answer: The most important consideration is adequate drainage holes in the bottom of the container. Without drainage holes, no amount of stones in the bottom will keep the roots of your tree out of stagnant water, which will eventually suffocate the roots and kill the tree. As long as the container has plenty of good drainage, you can fill the bottom with stones, up to about a third of the height of the container, then use amended garden soil to fill the rest of the container, up to about 3" from the rim. Dig a hole to plant the tree and then mulch over the surface of the soil after the tree has been installed.
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