You will have to ask Hitech about the 3D structure of this generation of clouds, he or Waffle built them. I'm using his clouds that are available from the menu. I have a restriction of making sure there is a minimum of 40 miles between logical blocks of clouds out of that menu so you don't take FPS hits processing two moving cloud groups. After that I have control of time duration, direction, alt, and speed of travel. The clouds do grow some as they travel and gain alt over a range you can define.
I chose cloud groups based on what kinds of clouds will generate at what elevations over the underlying landscape. I also chose 10k as the minimum alt after testing because any lower creates a sense of claustrophobia which gets worse if you enable shadows. The high alt cirrus layer I chose is the thinnest one because the thicker you make them, the more they add to visual confusion and claustrophobia when coupled with groups of clouds and cuts down on light in general to a degree.
The new cloud editor allows you to create your own clouds, so contact Hitech with any questions on that part of the new cloud editor. I do not know the procedure to have any of your own clouds used in the Melee arena. It's easier for me to use the existing menu of clouds knowing Hitech has passed them for use in the MA.
Don't shoot the messenger.....

Note: Clouds that move in from over an edge of the map are set to 12,000-15,000. Clouds that are near the opposite edge of the map and will pass off the map edge in transit are 10,000-13,000 to look like the land heat is raising up the clouds from over the water. Clouds inside of the four edges of the map passing over islands and water are 8,000-10,000. Having an issue with a sense of 2Dishness is an illusion because of how I chose to take the screen captures to show off Hitech's new clouds to this audience. And the 40 mile separation from other cloud blocks so you have nothing to use as a perspective. Also this map is an area of 250milesx250miles, in the real world often an area like that does not have large variations in cloud elevation unless you live next to a mountain range.
I found over the years I didn't like aspects of the game and Hitech had other things to deal with than my gripes. So I have given terrains a shot to solve some of my gripes and now clouds. Everyone is free to go for it and enchant the community with their vision of the game. I could not change the structure of the clouds if I wanted to for MA use, these is what we gots.