First you'd have to add and remove the ability 'Arav' to/from the dummy unit so that the unit doesn't use this flying height smoothing which is neat for normal flying units but usually screws up projectiles:
JASS:
call UnitAddAbility(u, 'Arav')
call UnitRemoveAbility(u, 'Arav')
Doing this will result in GetUnitFlyHeight() returning the unit's Z above the terrain.
As a unit's flying height is just a z-offset to the terrain under the unit you'd have to add the terrain height difference to the unit's flying height. If you're moving the projectile by hand (i.e. a periodic timer) you can just set the unit's flying height to
call SetUnitFlyHeight(u, GetUnitFlyHeight(u)+dz, 0) where dz is the z-difference of the current unit location and the location the unit is being moved to.
If you're not moving the projectile via timer though you might have to make a periodic timer and every now and then adjust the unit's flying height like described above.
You can also just use one of the projectile systems on this forum :).
