Sub-trim is what Futaba call's their servo centering function. It's a way to make up for the problem servo centering has with the teeth in the servo arm matching the teeth on the servo drive shaft. When you try to get the servo arm to make a perfect 90degree angle with the pushrod (the angle the arm makes with the servo is absolutely of no consequence) the arm usually won't match up with the drive shaft to give perfectly 90degrees. Also, some people like to have their trim levers at zero trim (a pretty good idea) and think the radio should give them a crutch to do that (a less than good idea). And the sub-trim can do that too.

You really want to make sure your sub-trim setting is centered for this exercise.