You gotta manually offset the emitters in the unit json. It's extremely tedious, but it's the easiest way. You could also try to make a new effect file so you can reload the effects automatically (one the file is saved and a new unit is created in the game) but that is also very tedious, as the hover effect mesh/model does not position itself the way you think it does (it needs to be rotated, which can only be done in the unit json).
That's done in the material and mask textures. Check out what I did for the legion hover tank: https://github.com/Legion-Expansion/Legion-Expansion/tree/master/art/textures/512/land/L_hover_tank The hover effect areas are pink on the mask map.
I could use some. Currently I'm having trouble getting the ai working. I'm just trying to see if I missed something critical in your instructions.