 So Blender is awesome, but your company requires you to use ZBrush, not a problem. If you're in ZBrush and you have your mesh separated by polygroups, under ZPlugin go to FBX Export, and under Options, check Export Polygroup as Matz. And in Substance, File, New, set your size and import as usual, then under Texture Settings, Bake, and under ID, set color source to Mesh ID and Polygroup. Okay, you're done. Now when you drag your material, just hold Control and apply it to whatever group you want. Hope that helps, and as always, hope you have a fantastic day, and I'll see you around.