Bringing in a file with different texture sets

Method 1, if your aim is to have a texture set for each material:

a. Before exporting from Blender assign materials to each surface and give each a unique name.

b. Unwrap ensuring their are no overlapped UVs within each texture

c. Export from Blender as FBX

d. Import to Substance painter (make sure Open GL is set as Normal Map Format) and you should have a texture set for each material

e. Bake the mesh maps for  Normal, World Space Normal, AO, Curvature, Position, Thickness

f. Paint / assign textures

g. Export texture sets

h. Use node wrangler in Blender to assign the texture maps and thereby replace the original material with those from Substance

Method 2 , If your aim is to paint/assign different materials in Painter but only have one texture set combining those materials

a. Unwrap in Blender ensuring their are no overlapped UVs across the model

b. Make a duplicate object

c. On one object assign materials to each part and give them different colours

d. On the duplicate assign a single material across the entire object

e. Export both from Blender as FBX and call the first for example object_high and the second object_low

f. Import object_low (i.e. the single material object) to Substance painter

g. Bake the maps and under baking set ID to Material Colour and High Definition Meshes to object_high (the object with the coloured materials assigned) Bake the mesh maps for  Normal, World Space Normal, ID, AO, Curvature, Position, Thickness

h. Paint / assign textures using the ID maps to separate the material sections. You can drop materials onto sections using Ctrl+Drag or add a mask with color selection using the ID maps

i. Export texture set

j. Use node wrangler in Blender to assign the texture map to the single material version and thereby replace the original material with those from Substance

Dave