Maybe I can explain it better. It was a multistem shrub. I cut off all the stems at the base of the plant except for the one that was growing straight up. The stems that were cut off at the base are now starting to regrow. Should I raise the dirt level in the container to cover them or just keep removing the foliage as it appears?

Did you find your answers yet? I would say go ahead and trim off those lower branches. From what I've read, it takes a few years to train into a tree form, hence the price of the tree form 'Limelight' at the nurseries. Hope you're taking pictures, I'd love to see the progress from year to year.

If you want to train this shrub to be a tree cut all the branches to the ground. When it starts to grow train one stem up a stick and remove all the others. All the growth will go into that one stem to form a tree. Once it get to the height you want stop training it, trim the leader and let it branch at the top of the trunk. You can remove the stick after a few years once the stem is nice and thick and can support the top.

Here is a link that might be useful: The Plant Hunter