Alright lets do this.
Step 1, create your map, use rpgmaker to design a basic building reference, once you have created a reference create an other version with no buildings on it, right click maps :save as image, bring both maps into gimp or photoshop
Step 2 find a building model pack, interior pack ect of what you are trying to design a layout for, import the 3D building into a 3D program of your choice, in my case I am going to use Daz3d
You will need to setup the building at an angle matching rpgmaker
You will need to create two renders one of the roof and one of the front facing at a slight angle,
Bring those renders into photoshop and combine them to create a roof that has a strait edges that matches the side of the building
Apply buildings to blank map and use the reference map to figure out building placement,
Go back into rpgmaker right click map set parallax, use either an invisible tile to set collision or use regions for collision
thats a very simplified version of how parallax maps like the ones in nadia are created.
as far as being able to walk behind buildings, that will require some more indepth work and use of plugins
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that video covers it.