All of what your asking can simply be done in the object editor:
Well if you made a custom unit as a normal ground unit, even if you change the model to a flying unit model, the editor will simply put it on the ground(since it is defined as a ground unit) this should be an easy fix. (for example lets say you chose the blademaster as your custom unit's base settings and then you changed his model to a dragon.. well the base settings are still set for the unit to be on a ground, so you must manually change this)
Change the following on your custom unit:
Movement - Height: to any number above 0 (depending on how far up you want your unit to be)
Combat - Targeted as: change form ground to air (unless you want your unit to still be targeted as ground)
Hope this helps,
Army_Strong