Using Autotile with 2.5d Zelda style view

Hi,

have been researching this but haven't quite found the answer I am looking for. Essentially, though I find the in built autotile excellent for a pure top down view (eg crimsonland), or side view platformer, I get a little confused when the view is 2.5d eg zelda, stardew valley, nuclear throne etc, which use horizontally viewed tiles and sprites to give the appearance of depth. I am finding it hard to make this work, as generally laying a floor tile will then require 2 tiles above it (eg a wall tile then a "roof tile"). Though its easy enough to lay all this tile by tile manually, is there a simple way to do this with autotiling? Hope I explained that properly, any help appreciated.
 
I just watched (what I think was) an official YOYO trailer for the autotile feature, and it shows the floor tiles being drawn with the walls being added by the autotile system, and the user manually adds in visible south facing wall tiles. So i guess essentially you would have to make rooms one tile taller than you want, then manually draw over the top row? Is this what everyone does?
 
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