During the root regeneration phase that follows transplanting a young tree, do not prune the top of the tree. Pruning at this point only serves to remove leave area and slow down root growth. A pecan trees will tell you when they are ready to be trained. Two to three years after transplanting, the top of the tree will suddenly explode with new shoot growth (especially with proper weed control and adequate soil nutrition). This is the tree's signal that the root system has become well established and the tree is ready to be trained.
Training young trees starts by applying the 2 foot rule right on the growing graft. In the photo at left, you can see that a vigorously growing seedling tree will push both the scion and stump sprouts to grow rapidly. Find the strongest growth shoot growing from the scion and prune all other out. This shoot will be the new central leader. Prune off all the stump sprouts unless your central leader has already grown 2 feet in height. Following the 2 foot rule, you can leave a lateral shoot on below the graft to help provide leaf area to support the root system (photo below).
Use a stake to train you central leader (I use bamboo). The stake also provides a place for birds to perch so they don't land on the tender new growth of the central leader and damage the growing point.
Training a young tree that grows rapidly is relatively easy using the 2 foot rule. It just requires paying attention to details and a monthly inspection (and pruning when necessary) of your trees from May thru July.
The last post in the training young trees series is Summing up