Lying down puts additional pressure on the lungs. This is because a person's own weight is pressing down on them. This makes it more difficult to breathe deeply and with the proper technique needed for inhaling neb meds. If she is more comfortable lying down, consider having her wear a mask, that way she's more likely to get all the benefit of the medication.
As Liza mentioned, lying back against the pillows is another resting position during nebs. That is better than lying down.
At this point, don't force the issue. As she gets older and can understand more, help her learn the importance of the meds and how important it is to inhale them properly in the right position.