Sounds like you'd want to use a negative flying height for that.
A unit's flying height is only considered if its movement type is Hover or Fly, but that should be fine for ghosts anyway. Ground units like Wisps and Banshees use Hover, while flying units use Fly.
Units that fly have a minimum flying height (Movement - Height Minimum) as well as their normal flying height (Movement - Height) so you'll need to experiment with those a bit. Set them to equal values, and set them so that your boss units are completely below ground at first.
Later, when you want them to rise, use the trigger action Animation - Change Unit Flying Height to bring them up to (or slightly above) ground level, which is height 0.0 for most unit models. Keep in mind that the "rate" value in that action represents how much height the unit should gain per second.