I tried both; results will depend greatly on the complexity of the mesh. If the vertices generally follow the shape of the skeleton (most of the body/armor/clothing meshes in Native), then yes, auto-assigning to the bones should be the way to go. But if you've got a model with protrusions (the hitatare model for Onin no Ran has long, hanging sleeves) or other complexities, then you're better off manually assigning verts to bones. I recommend trying the auto assign first, then make sure the assignments are the way you want them. It's a great tool to bang out a lot of meshes in a hurry.