Hi Phiro, having a separate material for every surface could work for simple models but it's likely to be inefficient for anything larger. The main way to set things up would be to set up a uvmapping which controls where polygons will paint into a texture map.

If Substance Painter does not have its own tools for setting up UV mapping and expects for it to already be set up, you could use one of the standalone uv mapping tools I linked to above to set it up.

- Michael