I use ID mapping to texture in Substance Painter and it is easiest if I delete all materials on export from Blender as FBX. I modified the existing FBX exporter to add an option to delete materials on export so that if I need to make changes to the model I don't have to undo/redo materials every time.
This is a very simple patch, any questions please contact me.
Me using it can be seen at: https://youtu.be/jVVa_eepk_A?t=4m55s