Texturing in UR from Substance Painter

So i have a mesh that that is one single mesh and i have different material groups assigned to different parts of the mesh. So the mesh itself was UVed in a way were different parts are a different material so if i stacked these UVs into one material group, they would grossly overlap. The texture would then spread across the entire mesh. So i make the next material and it overrides the last material. I cant seem to find a way to make these work though some of these tutorials. Does anyone know of a good Modo-Substance-UR4 work flow for this?