Multiple materials works a bit funny in substance painter, instead of treating them as multiple materials on the same texture sheet, it literally creates a separate texture sheet for each material, when you load a multimaterial object in you will see a list of the materials in the top right box, you have to work on each separately by clicking on the one you want to work on, which means if you want them on a single texture sheet you need to combione each one outside substance because substance doesn't do that.
When I use substance, in blender I just use one material for the whole model, then vertex paint each area I want different with a different colour, then when I import it into substance I use those colours as a colour ID and can paint each area separately, but still maintain just one sheet for all the materials, it's easier that way.
I will get round to finishing my workflow video soon I promise, and that will include a part on how to use the colour ID system for single texture sheets.
As to actual multi-texture models in the PBR version of GameGuru, not sure if that's implemented yet or not.
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