I have created this mesh which has (what I hope is) nice, even topology to use for a cloth simulation:
I also have this mesh which separates my object into different faces for which I want to apply different materials and textures:
At the moment they are both separate objects.
I'm not sure quite how to articulate this but I'm imagining that there might be a way to apply the materials and textures to the faces on the second mesh in a way that it will then map onto the first mesh during rendering without it physically effecting it's topology. So in other words to have one object with different "layers" all working together: one for the topology and physics of the object and one for the materials and textures.
Is this possible? If not then the only thing I can think of doing with my existing knowledge of Blender is to use the knife project tool to merge the two meshes together but I think that could get messy.