Wait now until late winter to fertilize as you don't want to encourage late season growth. The pecan should grow but you need to be sure the tree did not have a root encircling the flower pot as that would end up girdling (strangling) the tree in time as the root and trunk grow in diameter. It would be better to cut the root now and replant the tree.
You should not need to do anything to protect the maples over winter.
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