Put a large pot of water on to boil.
Cut sweet potatoes into 1 inch cubes.
Add sweet potatoes to boiling water and cook for 10 minutes. The sweet potato cubes should not be completely soft. Drain sweet potatoes after 10 minutes.
While sweet potatoes are boiling, dice onion and core and cut apples into 1/2 inch cubes.
Mix together salt, pepper, cinnamon, nutmeg, and ground thyme in small bowl.
Heat 2 tablespoons vegetable oil in large frying pan over medium-high heat.
Add drained sweet potatoes, apples, and onion to pan. Sprinkle with about half the spice mixture and stir vigorously.
Sprinkle with the other half of the spice mixture and stir again. You don't want the spices to clump up on the sweet potatoes or apples, but to be evenly distributed.
Continue to saute for 10 minutes. Add water and balsamic vinegar and mix well.
Remove from heat and serve immediately.